La recherche des motifs présentant de la fixation de Shavenbaby se fait en comparant les motifss ovoQ6 et svbF7 ( en les augmentant de 3kb ( start - 3kb / end + 3kb )) et les peaks Svb ( avec un peak-calling avec des sensibilités différentes ( q= 10-1 (stringent) ; q=10-4 (sensibily or low)) )
load("Myworkspace.RData")
svbF7_cons = read.table("/Users/alexmanchenoferris/Documents/motif_svb/svbF7_cons_flanked_dm6.bed")
ovoQ6_droso = read.table("/Users/alexmanchenoferris/Documents/motif_svb/ovoQ6_droso_flanked_dm6.bed")
svbF7_cons_gr = GRanges(seqnames = Rle(svbF7_cons$chr),
ranges=IRanges(start = svbF7_cons$start,end = svbF7_cons$end, names = paste(rep("svbF7_cons",nrow(svbF7_cons)),rownames(svbF7_cons), sep = "_")))
ovoQ6_droso_gr_unique = unique(GRanges(seqnames = Rle(ovoQ6_droso$chr),
ranges=IRanges(start = ovoQ6_droso$start,end = ovoQ6_droso$end, names = paste(rep("ovoQ6_droso",nrow(unique(ovoQ6_droso))),rownames(ovoQ6_droso), sep = "_"))))
SvbACT_peaks_low = read.table("/Users/alexmanchenoferris/Documents/Chipseq_ActRep/macs/low_quality/macs_1B_peaks.xls",sep = "\t", comment.char = "#", header = T, stringsAsFactors = F)
SvbACT.peaks_low = GRanges(seqnames = Rle(SvbACT_peaks_low[,1]),
ranges=IRanges(start = SvbACT_peaks_low[,2],end = SvbACT_peaks_low[,3], names = SvbACT_peaks_low[,10]),
strand = Rle(rep("*",nrow(SvbACT_peaks_low))),
score = SvbACT_peaks_low[,7],
fold_enrichment = SvbACT_peaks_low[,8])
SvbACT_peaks_embryo = read.table("/Users/alexmanchenoferris/Documents/Chipseq_ActRep/macs/embryo/macs_svb_01_peaks.xls",sep = "\t", comment.char = "#", header = T, stringsAsFactors = F)
SvbACT.peaks_embryo = GRanges(seqnames = Rle(SvbACT_peaks_embryo[,1]),
ranges=IRanges(start = SvbACT_peaks_embryo[,2],end = SvbACT_peaks_embryo[,3], names = SvbACT_peaks_embryo[,10]),
strand = Rle(rep("*",nrow(SvbACT_peaks_embryo))),
score = SvbACT_peaks_embryo[,7],
fold_enrichment = SvbACT_peaks_embryo[,8])
SvbACT_peaks_associated = read.table("/Users/alexmanchenoferris/Documents/ListeGene/peak_associed_geneDE/coordonnees_peak_associed_gene_diff_0-5kb.bed",sep = "\t", comment.char = "#", header = T, stringsAsFactors = F)
SvbACT.peaks_assiociated = GRanges(seqnames = Rle(SvbACT_peaks_associated[,1]),
ranges=IRanges(start = SvbACT_peaks_associated[,2],end = SvbACT_peaks_associated[,3], names = SvbACT_peaks_associated$names),
strand = Rle(rep("*",nrow(SvbACT_peaks_associated))),
score = SvbACT_peaks_associated$scores,
fold_enrichment = SvbACT_peaks_associated$fold)
promoters_directgenes = read.table("/Users/alexmanchenoferris/Documents/ListeGene/direct_target_gene_coordonnees/promoters_gene_0_5b_tab.bed")
colnames(promoters_directgenes) = c("chr","start","end","length","strand")
promoters_directgenes_gr = GRanges(seqnames = Rle(promoters_directgenes$chr),
ranges=IRanges(start = promoters_directgenes$start,end = promoters_directgenes$end, names = paste(rep("promoters",nrow(promoters_directgenes)),rownames(promoters_directgenes), sep = "_")))
# en flankant les motifs de 300kb ( taille moyenne des pics )
svbF7_cons_300 = read.table("/Users/alexmanchenoferris/Documents/motif_svb/300pb/svbF7_cons.bed")
ovoQ6_droso_300 = read.table("/Users/alexmanchenoferris/Documents/motif_svb/300pb/ovoQ6.bed")
colnames(ovoQ6_droso_300) = c("chr","start","end")
colnames(svbF7_cons_300) = c("chr","start","end")
svbF7_cons_gr_300 = GRanges(seqnames = Rle(svbF7_cons_300$chr),
ranges=IRanges(start = svbF7_cons_300$start,end = svbF7_cons_300$end, names = paste(rep("svbF7_cons",nrow(svbF7_cons_300)),rownames(svbF7_cons_300), sep = "_")))
ovoQ6_droso_gr_unique_300 = unique(GRanges(seqnames = Rle(ovoQ6_droso_300$chr),
ranges=IRanges(start = ovoQ6_droso_300$start,end = ovoQ6_droso_300$end, names = paste(rep("ovoQ6_droso",nrow(unique(ovoQ6_droso_300))),rownames(ovoQ6_droso_300), sep = "_"))))
## $p.value
## SvbAct ovoQ6 svbF7 pval
## [1,] 0 1 1 NaN
## [2,] 1 0 1 NaN
## [3,] 1 1 0 NaN
##
## $vennCounts
## SvbAct ovoQ6 svbF7 Counts count.B1.peaks count.ovoQ6_droso_gr_unique
## [1,] 0 0 0 -45933 0 0
## [2,] 0 0 1 182 0 0
## [3,] 0 1 0 39903 0 39903
## [4,] 0 1 1 1223 0 8039
## [5,] 1 0 0 829 829 0
## [6,] 1 0 1 63 94 0
## [7,] 1 1 0 3076 3103 10374
## [8,] 1 1 1 757 1486 7207
## count.svbF7_cons_gr
## [1,] 0
## [2,] 182
## [3,] 0
## [4,] 1223
## [5,] 0
## [6,] 69
## [7,] 0
## [8,] 880
## attr(,"class")
## [1] "VennCounts"
## $p.value
## SvbAct ovoQ6 pval
## [1,] 1 1 NaN
##
## $vennCounts
## SvbAct ovoQ6 Counts count.B1.peaks count.ovoQ6_droso_gr_unique
## [1,] 0 0 -55740 0 0
## [2,] 0 1 50359 0 50359
## [3,] 1 0 925 925 0
## [4,] 1 1 4556 4587 15164
## attr(,"class")
## [1] "VennCounts"
## $p.value
## SvbAct svbF7 pval
## [1,] 1 1 NaN
##
## $vennCounts
## SvbAct svbF7 Counts count.B1.peaks count.svbF7_cons_gr
## [1,] 0 0 -6859 0 0
## [2,] 0 1 1751 0 1751
## [3,] 1 0 4652 4652 0
## [4,] 1 1 556 860 603
## attr(,"class")
## [1] "VennCounts"
svbF7_motifs_unbound = as.data.frame(svbF7_cons_gr_svb_bind_overlap$peaklist$svbF7_cons_gr)
svbF7_motifs_bound = as.data.frame(svbF7_cons_gr_svb_bind_overlap$peaklist$`B1.peaks///svbF7_cons_gr`)
ovoQ6_motifs_unbound = as.data.frame(ovoQ6_droso_svb_bind_overlap$peaklist$ovoQ6_droso_gr_unique)
ovoQ6_motifs_bound = as.data.frame(ovoQ6_droso_svb_bind_overlap$peaklist$`B1.peaks///ovoQ6_droso_gr_unique`)
## $p.value
## SvbAct ovoQ6.motif svbF7 pval
## [1,] 0 1 1 NaN
## [2,] 1 0 1 NaN
## [3,] 1 1 0 NaN
##
## $vennCounts
## SvbAct ovoQ6.motif svbF7 Counts count.SvbACT.peaks_low
## [1,] 0 0 0 -44598 0
## [2,] 0 0 1 175 0
## [3,] 0 1 0 37562 0
## [4,] 0 1 1 1119 0
## [5,] 1 0 0 1009 1009
## [6,] 1 0 1 70 111
## [7,] 1 1 0 3907 3946
## [8,] 1 1 1 856 1872
## count.ovoQ6_droso_gr_unique count.svbF7_cons_gr
## [1,] 0 0
## [2,] 0 175
## [3,] 37562 0
## [4,] 7263 1119
## [5,] 0 0
## [6,] 0 76
## [7,] 12383 0
## [8,] 8315 984
## attr(,"class")
## [1] "VennCounts"
## $p.value
## SvbAct ovoQ6 pval
## [1,] 1 1 NaN
##
## $vennCounts
## SvbAct ovoQ6 Counts count.SvbACT.peaks_low count.ovoQ6_droso_gr_unique
## [1,] 0 0 -54247 0 0
## [2,] 0 1 47459 0 47459
## [3,] 1 0 1121 1121 0
## [4,] 1 1 5767 5817 18064
## attr(,"class")
## [1] "VennCounts"
## $p.value
## SvbAct svbF7 pval
## [1,] 1 1 NaN
##
## $vennCounts
## SvbAct svbF7 Counts count.SvbACT.peaks_low count.svbF7_cons_gr
## [1,] 0 0 -8112 0 0
## [2,] 0 1 1671 0 1671
## [3,] 1 0 5912 5912 0
## [4,] 1 1 629 1026 683
## attr(,"class")
## [1] "VennCounts"
## $p.value
## SvbAct ovoQ6 svbF7 pval
## [1,] 0 1 1 NaN
## [2,] 1 0 1 NaN
## [3,] 1 1 0 NaN
##
## $vennCounts
## SvbAct ovoQ6 svbF7 Counts count.SvbACT.peaks_embryo
## [1,] 0 0 0 -42353 0
## [2,] 0 0 1 151 0
## [3,] 0 1 0 34214 0
## [4,] 0 1 1 672 0
## [5,] 1 0 0 1228 1228
## [6,] 1 0 1 95 133
## [7,] 1 1 0 4855 4915
## [8,] 1 1 1 1238 2430
## count.ovoQ6_droso_gr_unique count.svbF7_cons_gr
## [1,] 0 0
## [2,] 0 151
## [3,] 34214 0
## [4,] 4420 672
## [5,] 0 0
## [6,] 0 100
## [7,] 15239 0
## [8,] 11650 1431
## attr(,"class")
## [1] "VennCounts"
## $p.value
## SvbAct ovoQ6 pval
## [1,] 1 1 NaN
##
## $vennCounts
## SvbAct ovoQ6 Counts count.SvbACT.peaks_embryo count.ovoQ6_droso_gr_unique
## [1,] 0 0 -50909 0 0
## [2,] 0 1 42375 0 42375
## [3,] 1 0 1365 1365 0
## [4,] 1 1 7269 7341 23148
## attr(,"class")
## [1] "VennCounts"
## $p.value
## SvbAct svbF7 pval
## [1,] 1 1 NaN
##
## $vennCounts
## SvbAct svbF7 Counts count.SvbACT.peaks_embryo count.svbF7_cons_gr
## [1,] 0 0 -9557 0 0
## [2,] 0 1 1359 0 1359
## [3,] 1 0 7379 7379 0
## [4,] 1 1 919 1327 995
## attr(,"class")
## [1] "VennCounts"
## $p.value
## SvbAct ovoQ6 svbF7 pval
## [1,] 0 1 1 NaN
## [2,] 1 0 1 NaN
## [3,] 1 1 0 NaN
##
## $vennCounts
## SvbAct ovoQ6 svbF7 Counts count.unique.SvbACT.peaks_assiociated.
## [1,] 0 0 0 -52876 0
## [2,] 0 0 1 245 0
## [3,] 0 1 0 50359 0
## [4,] 0 1 1 2012 0
## [5,] 1 0 0 67 67
## [6,] 1 0 1 5 5
## [7,] 1 1 0 220 220
## [8,] 1 1 1 68 93
## count.ovoQ6_droso_gr_unique count.svbF7_cons_gr
## [1,] 0 0
## [2,] 0 245
## [3,] 50359 0
## [4,] 13531 2012
## [5,] 0 0
## [6,] 0 6
## [7,] 906 0
## [8,] 727 91
## attr(,"class")
## [1] "VennCounts"
## $p.value
## SvbAct ovoQ6 pval
## [1,] 1 1 NaN
##
## $vennCounts
## SvbAct ovoQ6 Counts count.unique.SvbACT.peaks_assiociated.
## [1,] 0 0 -64497 0
## [2,] 0 1 64212 0
## [3,] 1 0 72 72
## [4,] 1 1 313 313
## count.ovoQ6_droso_gr_unique
## [1,] 0
## [2,] 64212
## [3,] 0
## [4,] 1311
## attr(,"class")
## [1] "VennCounts"
## $p.value
## SvbAct svbF7 pval
## [1,] 1 1 NaN
##
## $vennCounts
## SvbAct svbF7 Counts count.unique.SvbACT.peaks_assiociated.
## [1,] 0 0 -2574 0
## [2,] 0 1 2298 0
## [3,] 1 0 328 328
## [4,] 1 1 48 57
## count.svbF7_cons_gr
## [1,] 0
## [2,] 2298
## [3,] 0
## [4,] 56
## attr(,"class")
## [1] "VennCounts"
## $p.value
## SvbAct ovoQ6 svbF7 pval
## [1,] 0 1 1 NaN
## [2,] 1 0 1 NaN
## [3,] 1 1 0 NaN
##
## $vennCounts
## SvbAct ovoQ6 svbF7 Counts count.unique.promoters_directgenes_gr.
## [1,] 0 0 0 -52748 0
## [2,] 0 0 1 249 0
## [3,] 0 1 0 50336 0
## [4,] 0 1 1 2021 0
## [5,] 1 0 0 31 31
## [6,] 1 0 1 2 2
## [7,] 1 1 0 158 158
## [8,] 1 1 1 51 56
## count.ovoQ6_droso_gr_unique count.svbF7_cons_gr
## [1,] 0 0
## [2,] 0 249
## [3,] 50336 0
## [4,] 13587 2021
## [5,] 0 0
## [6,] 0 2
## [7,] 921 0
## [8,] 679 82
## attr(,"class")
## [1] "VennCounts"
## $p.value
## SvbAct ovoQ6 pval
## [1,] 1 1 NaN
##
## $vennCounts
## SvbAct ovoQ6 Counts count.unique.promoters_directgenes_gr.
## [1,] 0 0 -64383 0
## [2,] 0 1 64236 0
## [3,] 1 0 33 33
## [4,] 1 1 214 214
## count.ovoQ6_droso_gr_unique
## [1,] 0
## [2,] 64236
## [3,] 0
## [4,] 1287
## attr(,"class")
## [1] "VennCounts"
## $p.value
## SvbAct svbF7 pval
## [1,] 1 1 NaN
##
## $vennCounts
## SvbAct svbF7 Counts count.unique.promoters_directgenes_gr.
## [1,] 0 0 -2463 0
## [2,] 0 1 2317 0
## [3,] 1 0 216 216
## [4,] 1 1 30 31
## count.svbF7_cons_gr
## [1,] 0
## [2,] 2317
## [3,] 0
## [4,] 37
## attr(,"class")
## [1] "VennCounts"
J’utilise la fonction de bedtools hypergéométrique avec comme option " a : les SvbF7 motif b : les marque d’histones et l’overlap est de 1bp
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 unbound | 578 | 811 |
| absent svbF7 unbound | 8188 | 5736 |
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 bound | 633 | 0 |
| absent svbF7 bound | 8139 | 6732 |
pvalue_fixe = phyper(633 - 1, 486, 15504 - 486, 8772)
pvalue_nonfixe = phyper(578 - 1, 1389, 15313 - 1389, 8766)
presence = c(633,8139)
absence = c(0,6732)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me1_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me1_fixe)
presence = c(578,8188)
absence = c(811,5736)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me1_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me1_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 4.409109110^{-35}
La pvalue du test de fisher pour les motifs fixé est de 1.024422510^{-161} Celle du test de fisher pour les motifs non fixé est de 1.413975810^{-34}`
total_svbF7_unbound = 578 + 811
total_svbF7_bound = 633
percent_svbf7_H3K4me1_unbound = round(100 * 578 / total_svbF7_unbound, 2 )
percent_svbf7_unbound_without_H3K4me1 = round(100 * 811 / total_svbF7_unbound, 2 )
percent_svbf7_H3K4me1_bound = round(100 * 633 / total_svbF7_bound, 2 )
percent_svbf7_bound_without_H3K4me1 = round(100 * 0 / total_svbF7_bound, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me1_absent = c(percent_svbf7_bound_without_H3K4me1,percent_svbf7_unbound_without_H3K4me1)
H3K4me1_present = c(percent_svbf7_H3K4me1_bound,percent_svbf7_H3K4me1_unbound)
data_H3K4me1 = data.frame(etat_svb,H3K4me1_absent,H3K4me1_present)
datatable(data_H3K4me1,rownames = F,filter = "none",colnames = c("Regions without H3K4me1","Regions with H3K4me1" ))
fig3 = plot_ly(data_H3K4me1, x = ~etat_svb,y = ~H3K4me1_absent, type = "bar",name = "H3K4me1 absent", color = I("grey"))
fig3 = fig3 %>% add_trace(y = ~H3K4me1_present, name = "H3K4me1 present", color = I("orange"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig3
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 unbound | 149 | 1240 |
| absent svbF7 unbound | 4658 | 10496 |
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 bound | 359 | 127 |
| absent svbF7 bound | 4449 | 11833 |
pvalue_fixe = phyper(633 - 1, 486, 15504 - 486, 8772)
pvalue_nonfixe = phyper(149 - 1, 1389, 16543 - 1389, 4807)
presence = c(359,4449)
absence = c(127,11833)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me3_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me3_fixe)
presence = c(149,4658)
absence = c(1240,10496)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me3_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me3_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 2.377300810^{-66}
La pvalue du test de fisher pour les motifs fixé est de 2.264480710^{-97} Celle du test de fisher pour les motifs non fixé est de 1.30972510^{-65}`
total_svbF7_unbound_H3K4me3 = 149 + 1240
total_svbF7_bound_H3K4me3 = 359 + 127
percent_svbf7_H3K4me3_unbound = round(100 * 149 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_unbound_without_H3K4me3 = round(100 * 1240 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_H3K4me3_bound = round(100 * 359 / total_svbF7_bound_H3K4me3, 2 )
percent_svbf7_bound_without_H3K4me3 = round(100 * 127 / total_svbF7_bound_H3K4me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me3_absent = c(percent_svbf7_bound_without_H3K4me3,percent_svbf7_unbound_without_H3K4me3)
H3K4me3_present = c(percent_svbf7_H3K4me3_bound,percent_svbf7_H3K4me3_unbound)
data_H3K4me3 = data.frame(etat_svb,H3K4me3_absent,H3K4me3_present)
datatable(data_H3K4me3,rownames = F,filter = "none",colnames = c("Regions without H3K4me3","Regions with H3K4me3" ))
fig4 = plot_ly(data_H3K4me3, x = ~etat_svb,y = ~H3K4me3_absent, type = "bar",name = "H3K4me3 absent", color = I("grey"))
fig4 = fig4 %>% add_trace(y = ~H3K4me3_present, name = "H3K4me3 present", color = I("pink"))
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig4
total_K4me1_S2 = 8782
total_K4me3_S2 = 4812
rapp_fixe = round((contingence_H3K4me1_fixe[1,1] / total_K4me1_S2 ) / (contingence_H3K4me3_fixe[1,1] / total_K4me3_S2),2)
rapp_nonfixe = round((contingence_H3K4me1_nonfixe[1,1] / total_K4me1_S2) / (contingence_H3K4me3_nonfixe[1,1] / total_K4me3_S2) ,2)
Il y a 0.97 fois de H3K4me1 que de H3K4me3 fixé.
Il y a 2.13 fois de H3K4me1 que de H3K4me3 non fixé.
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 unbound | 286 | 1103 |
| absent svbF7 unbound | 4862 | 7327 |
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 bound | 435 | 51 |
| absent svbF7 bound | 4718 | 8527 |
pvalue_fixe = phyper(435 - 1, 486, 13731 - 486, 5153)
pvalue_nonfixe = phyper(286 - 1, 1389, 13578 - 1389, 5148)
presence = c(435,4718)
absence = c(51,8527)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27ac_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27ac_fixe)
presence = c(286,4862)
absence = c(1103,7327)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27ac_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27ac_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 6.787045710^{-49}
La pvalue du test de fisher pour les motifs fixé est de 4.16793910^{-131} Celle du test de fisher pour les motifs non fixé est de 2.604877810^{-48}`
total_svbF7_unbound_H3K27ac = 286 + 1103
total_svbF7_bound_H3K27ac = 435 + 51
percent_svbf7_H3K27ac_unbound = round(100 * 286 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_unbound_without_H3K27ac = round(100 * 1103 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_H3K27ac_bound = round(100 * 435 / total_svbF7_bound_H3K27ac, 2 )
percent_svbf7_bound_without_H3K27ac = round(100 * 51 / total_svbF7_bound_H3K27ac, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K27ac_absent = c(percent_svbf7_bound_without_H3K27ac,percent_svbf7_unbound_without_H3K27ac)
H3K27ac_present = c(percent_svbf7_H3K27ac_bound,percent_svbf7_H3K27ac_unbound)
data_H3K27ac = data.frame(etat_svb,H3K27ac_absent,H3K27ac_present)
datatable(data_H3K27ac,rownames = F,filter = "none",colnames = c("Regions without H3K27ac","Regions with H3K27ac" ))
fig1 = plot_ly(data_H3K27ac, x = ~etat_svb,y = ~H3K27ac_absent, type = "bar",name = "H3K27ac absent", color = I("grey"))
fig1 = fig1 %>% add_trace(y = ~H3K27ac_present, name = "H3K27ac present", color = I("blue"))
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb")
fig1
fig1 = plot_ly(data_H3K27ac, x = ~etat_svb,y = ~H3K27ac_absent, type = "bar",name = "H3K27ac absent", color = I("grey"))
fig1 = fig1 %>% add_trace(y = ~H3K27ac_present, name = "H3K27ac present", color = I("blue"))
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig1
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 unbound | 1868 | 0 |
| absent svbF7 unbound | 11567 | 4071 |
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 bound | 311 | 175 |
| absent svbF7 bound | 13127 | 4145 |
pvalue_fixe = phyper(311 - 1, 486, 17758 - 486, 13438)
pvalue_nonfixe = phyper(286 - 1, 1389, 13578 - 1389, 5148)
presence = c(311,13127)
absence = c(175,4145)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27me3_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27me3_fixe)
presence = c(1868,11567)
absence = c(0,4071)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27me3_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27me3_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1.97262510^{-9} Celle du test de hypergéométrique pour les motifs non fixé est de 6.787045710^{-49}
La pvalue du test de fisher pour les motifs fixé est de 5.596902110^{-9} Celle du test de fisher pour les motifs non fixé est de 2.022617710^{-229}`
total_svbF7_unbound_H3K27me3 = 1868 + 0
total_svbF7_bound_H3K27me3 = 311 + 175
percent_svbf7_H3K27me3_unbound = round(100 * 1868 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_unbound_without_H3K27me3 = round(100 * 0 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_H3K27me3_bound = round(100 * 311 / total_svbF7_bound_H3K27me3, 2 )
percent_svbf7_bound_without_H3K27me3 = round(100 * 175 / total_svbF7_bound_H3K27me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K27me3_absent = c(percent_svbf7_bound_without_H3K27me3,percent_svbf7_unbound_without_H3K27me3)
H3K27me3_present = c(percent_svbf7_H3K27me3_bound,percent_svbf7_H3K27me3_unbound)
data_H3K27me3 = data.frame(etat_svb,H3K27me3_absent,H3K27me3_present)
datatable(data_H3K27me3,rownames = F,filter = "none",colnames = c("Regions without H3K27me3","Regions with H3K27me3" ))
fig2 = plot_ly(data_H3K27me3, x = ~etat_svb,y = ~H3K27me3_absent, type = "bar",name = "H3K27me3 absent", color = I("grey"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_present, name = "H3K27me3 present", color = I("purple"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig2
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 unbound | 514 | 813 |
| absent svbF7 unbound | 8252 | 5729 |
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 bound | 698 | 0 |
| absent svbF7 bound | 8074 | 6722 |
pvalue_fixe = phyper(698 - 1, 549, 15494 - 549, 8772)
pvalue_nonfixe = phyper(514 - 1, 1327, 15308 - 1327, 8766)
presence = c(698,8074)
absence = c(0,6722)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me1_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me1_fixe)
presence = c(514,8252)
absence = c(813,5729)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me1_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me1_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 3.231743410^{-46}
La pvalue du test de fisher pour les motifs fixé est de 1.39957510^{-178} Celle du test de fisher pour les motifs non fixé est de 1.266940710^{-45}`
total_svbF7_unbound = 514 + 813
total_svbF7_bound = 698
percent_svbf7_H3K4me1_unbound = round(100 * 514 / total_svbF7_unbound, 2 )
percent_svbf7_unbound_without_H3K4me1 = round(100 * 813 / total_svbF7_unbound, 2 )
percent_svbf7_H3K4me1_bound = round(100 * 698 / total_svbF7_bound, 2 )
percent_svbf7_bound_without_H3K4me1 = round(100 * 0 / total_svbF7_bound, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me1_absent = c(percent_svbf7_bound_without_H3K4me1,percent_svbf7_unbound_without_H3K4me1)
H3K4me1_present = c(percent_svbf7_H3K4me1_bound,percent_svbf7_H3K4me1_unbound)
data_H3K4me1 = data.frame(etat_svb,H3K4me1_absent,H3K4me1_present)
datatable(data_H3K4me1,rownames = F,filter = "none", colnames = c("Regions without H3K4me1","Regions with H3K4me1" ))
fig3 = plot_ly(data_H3K4me1, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig3 = fig3 %>% add_trace(y = ~H3K4me1_absent, name = "H3K4me1 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig3
data_H3K4me1 = data.frame(etat_svb,H3K4me1_absent,H3K4me1_present)
datatable(data_H3K4me1,rownames = F,filter = "none", colnames = c("Regions without H3K4me1","Regions with H3K4me1" ))
fig3 = plot_ly(data_H3K4me1, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig3 = fig3 %>% add_trace(y = ~H3K4me1_absent, name = "H3K4me1 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb")
fig3
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 unbound | 121 | 1206 |
| absent svbF7 unbound | 4686 | 10524 |
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 bound | 388 | 161 |
| absent svbF7 bound | 4420 | 11787 |
pvalue_fixe = phyper(388 - 1, 549, 16756 - 549, 4808)
pvalue_nonfixe = phyper(121 - 1, 1327, 16537 - 1327, 4807)
presence = c(388,4420)
absence = c(161,11787)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me3_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me3_fixe)
presence = c(121,4686)
absence = c(1206,10524)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me3_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me3_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 2.348151110^{-76}
La pvalue du test de fisher pour les motifs fixé est de 2.414317810^{-95} Celle du test de fisher pour les motifs non fixé est de 1.779050610^{-75}`
total_svbF7_unbound_H3K4me3 = 121 + 1206
total_svbF7_bound_H3K4me3 = 388 + 161
percent_svbf7_H3K4me3_unbound = round(100 * 121 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_unbound_without_H3K4me3 = round(100 * 1206 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_H3K4me3_bound = round(100 * 388 / total_svbF7_bound_H3K4me3, 2 )
percent_svbf7_bound_without_H3K4me3 = round(100 * 161 / total_svbF7_bound_H3K4me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me3_absent = c(percent_svbf7_bound_without_H3K4me3,percent_svbf7_unbound_without_H3K4me3)
H3K4me3_present = c(percent_svbf7_H3K4me3_bound,percent_svbf7_H3K4me3_unbound)
data_H3K4me3 = data.frame(etat_svb,H3K4me3_absent,H3K4me3_present)
datatable(data_H3K4me3,rownames = F,filter = "none",colnames = c("Regions without H3K4me3","Regions with H3K4me3" ))
fig4 = plot_ly(data_H3K4me3, x = ~etat_svb,y = ~H3K4me3_present, type = "bar",name = "H3K4me3 present", color = I("pink"))
fig4 = fig4 %>% add_trace(y = ~H3K4me3_absent, name = "H3K4me3 absent", color = I("grey"))
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig4
fig4 = plot_ly(data_H3K4me3, x = ~etat_svb,y = ~H3K4me3_present, type = "bar",name = "H3K4me3 present", color = I("pink"))
fig4 = fig4 %>% add_trace(y = ~H3K4me3_absent, name = "H3K4me3 absent", color = I("grey"))
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb")
fig4
total_K4me1_S2 = 8782
total_K4me3_S2 = 4812
rapp_fixe = round((contingence_H3K4me1_fixe[1,1] / total_K4me1_S2 ) / (contingence_H3K4me3_fixe[1,1] / total_K4me3_S2),2)
rapp_nonfixe = round((contingence_H3K4me1_nonfixe[1,1] / total_K4me1_S2) / (contingence_H3K4me3_nonfixe[1,1] / total_K4me3_S2) ,2)
Il y a 0.99 fois de H3K4me1 que de H3K4me3 fixé.
Il y a 2.33 fois de H3K4me1 que de H3K4me3 non fixé.
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 unbound | 244 | 1083 |
| absent svbF7 unbound | 4904 | 7343 |
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 bound | 478 | 71 |
| absent svbF7 bound | 4675 | 8500 |
pvalue_fixe = phyper(478 - 1, 549, 13724 - 549, 5153)
pvalue_nonfixe = phyper(244 - 1, 1327, 13574 - 1327, 5148)
presence = c(478,4675)
absence = c(71,8500)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27ac_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27ac_fixe)
presence = c(244,4904)
absence = c(1083,7343)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27ac_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27ac_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 1.425593210^{-59}
La pvalue du test de fisher pour les motifs fixé est de 2.973567510^{-133} Celle du test de fisher pour les motifs non fixé est de 8.220511410^{-59}`
total_svbF7_unbound_H3K27ac = 244 + 1083
total_svbF7_bound_H3K27ac = 478 + 71
percent_svbf7_H3K27ac_unbound = round(100 * 244 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_unbound_without_H3K27ac = round(100 * 1083 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_H3K27ac_bound = round(100 * 478 / total_svbF7_bound_H3K27ac, 2 )
percent_svbf7_bound_without_H3K27ac = round(100 * 71 / total_svbF7_bound_H3K27ac, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K27ac_absent = c(percent_svbf7_bound_without_H3K27ac,percent_svbf7_unbound_without_H3K27ac)
H3K27ac_present = c(percent_svbf7_H3K27ac_bound,percent_svbf7_H3K27ac_unbound)
data_H3K27ac = data.frame(etat_svb,H3K27ac_absent,H3K27ac_present)
datatable(data_H3K27ac,rownames = F,filter = "none",colnames = c("Regions without H3K27ac","Regions with H3K27ac" ))
# fig1 = plot_ly(data_H3K27ac, x = ~etat_svb,y = ~H3K27ac_absent, type = "bar",name = "H3K27ac absent")
# fig1 = fig1 %>% add_trace(y = ~H3K27ac_present, name = "H3K27ac present")
# fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
# fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb")
# fig1
fig1 = plot_ly(data_H3K27ac, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig1 = fig1 %>% add_trace(y = ~H3K27ac_absent, name = "H3K27ac absent", color = I("grey"))
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig1
fig1 = plot_ly(data_H3K27ac, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig1 = fig1 %>% add_trace(y = ~H3K27ac_absent, name = "H3K27ac absent", color = I("grey"))
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb")
fig1
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 unbound | 1791 | 0 |
| absent svbF7 unbound | 11644 | 4065 |
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 bound | 392 | 71 |
| absent svbF7 bound | 13046 | 4151 |
pvalue_fixe = phyper(392 - 1, 549, 17746 - 549, 13438)
pvalue_nonfixe = phyper(1791 - 1, 1327, 17500 - 1327, 13435)
presence = c(392,13046)
absence = c(71,4151)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27me3_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27me3_fixe)
presence = c(1791,11644)
absence = c(0,4065)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27me3_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27me3_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 0.0079173 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 5.493538610^{-6} Celle du test de fisher pour les motifs non fixé est de 4.53427810^{-219}`
total_svbF7_unbound_H3K27me3 = 1791 + 0
total_svbF7_bound_H3K27me3 = 392 + 157
percent_svbf7_H3K27me3_unbound = round(100 * 1791 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_unbound_without_H3K27me3 = round(100 * 0 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_H3K27me3_bound = round(100 * 392 / total_svbF7_bound_H3K27me3, 2 )
percent_svbf7_bound_without_H3K27me3 = round(100 * 157 / total_svbF7_bound_H3K27me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K27me3_absent = c(percent_svbf7_bound_without_H3K27me3,percent_svbf7_unbound_without_H3K27me3)
H3K27me3_present = c(percent_svbf7_H3K27me3_bound,percent_svbf7_H3K27me3_unbound)
data_H3K27me3 = data.frame(etat_svb,H3K27me3_absent,H3K27me3_present)
datatable(data_H3K27me3,rownames = F,filter = "none",colnames = c("Regions without H3K27me3","Regions with H3K27me3" ))
fig2 = plot_ly(data_H3K27me3, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color =I("purple"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_absent, name = "H3K27me3 absent",color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig2
fig2 = plot_ly(data_H3K27me3, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color =I("purple"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_absent, name = "H3K27me3 absent",color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb")
fig2
Je regarde ici l’enrichisement en histones des motifs de Svb en présence des différentes formes de Svb ( Act/ Rep) et Ctrl
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 unbound | 818 | 571 |
| absent svbF7 unbound | 9368 | 4332 |
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 bound | 698 | 0 |
| absent svbF7 bound | 9498 | 5082 |
pvalue_fixe = phyper(698 - 1, 486, 15278 - 486, 10196)
pvalue_nonfixe = phyper(818 - 1, 1389, 15089 - 1389, 10186)
presence = c(698,0)
absence = c(9498,5082)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me1_fixe_ctrl = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me1_fixe_ctrl)
presence = c(818,9368)
absence = c(571,4332)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me1_nonfixe_ctrl = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me1_nonfixe_ctrl)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 6.137004310^{-13}
La pvalue du test de fisher pour les motifs fixé est de 1.112238610^{-126} Celle du test de fisher pour les motifs non fixé est de 1.73553510^{-12}`
total_svbF7_unbound = 818 + 571
total_svbF7_bound = 698 + 0
percent_svbf7_H3K4me1_unbound = round(100 * 818 / total_svbF7_unbound, 2 )
percent_svbf7_unbound_without_H3K4me1 = round(100 * 571 / total_svbF7_unbound, 2 )
percent_svbf7_H3K4me1_bound = round(100 * 698 / total_svbF7_bound, 2 )
percent_svbf7_bound_without_H3K4me1 = round(100 * 0 / total_svbF7_bound, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me1_absent = c(percent_svbf7_bound_without_H3K4me1,percent_svbf7_unbound_without_H3K4me1)
H3K4me1_present = c(percent_svbf7_H3K4me1_bound,percent_svbf7_H3K4me1_unbound)
data_H3K4me1_ctrl = data.frame(etat_svb,H3K4me1_absent,H3K4me1_present)
datatable(data_H3K4me1_ctrl,rownames = F,filter = "none", colnames = c("Regions without H3K4me1","Regions with H3K4me1" ))
fig3 = plot_ly(data_H3K4me1_ctrl, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig3 = fig3 %>% add_trace(y = ~H3K4me1_absent, name = "H3K4me1 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb (Ctrl condition)", barmode = "stack")
fig3
fig3 = plot_ly(data_H3K4me1_ctrl, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig3 = fig3 %>% add_trace(y = ~H3K4me1_absent, name = "H3K4me1 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb (Ctrl condition)")
fig3
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 unbound | 988 | 401 |
| absent svbF7 unbound | 11249 | 0 |
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 bound | 753 | 0 |
| absent svbF7 bound | 11497 | 3863 |
pvalue_fixe = phyper(753 - 1, 486, 16113 - 486, 12250)
pvalue_nonfixe = phyper(988 - 1, 1389, 15904 - 1389, 12237)
presence = c(753,11497)
absence = c(0,3863)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me1_fixe_act = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me1_fixe_act)
presence = c(988,11249)
absence = c(0,401)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me1_nonfixe_act = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me1_nonfixe_act)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 6.005383710^{-8}
La pvalue du test de fisher pour les motifs fixé est de 1.450122910^{-92} Celle du test de fisher pour les motifs non fixé est de 6.41756610^{-15}`
total_svbF7_unbound = 988 + 401
total_svbF7_bound = 753 + 0
percent_svbf7_H3K4me1_unbound = round(100 * 988 / total_svbF7_unbound, 2 )
percent_svbf7_unbound_without_H3K4me1 = round(100 * 401 / total_svbF7_unbound, 2 )
percent_svbf7_H3K4me1_bound = round(100 * 753 / total_svbF7_bound, 2 )
percent_svbf7_bound_without_H3K4me1 = round(100 * 0 / total_svbF7_bound, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me1_absent = c(percent_svbf7_bound_without_H3K4me1,percent_svbf7_unbound_without_H3K4me1)
H3K4me1_present = c(percent_svbf7_H3K4me1_bound,percent_svbf7_H3K4me1_unbound)
data_H3K4me1_act = data.frame(etat_svb,H3K4me1_absent,H3K4me1_present)
datatable(data_H3K4me1_act,rownames = F,filter = "none", colnames = c("Regions without H3K4me1","Regions with H3K4me1" ))
fig3 = plot_ly(data_H3K4me1_act, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig3 = fig3 %>% add_trace(y = ~H3K4me1_absent, name = "H3K4me1 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb (Act condition)", barmode = "stack")
fig3
fig3 = plot_ly(data_H3K4me1_act, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig3 = fig3 %>% add_trace(y = ~H3K4me1_absent, name = "H3K4me1 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb (Act condition)")
fig3
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 unbound | 920 | 469 |
| absent svbF7 unbound | 10874 | 3453 |
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 bound | 745 | 0 |
| absent svbF7 bound | 11057 | 4118 |
pvalue_fixe = phyper(745 - 1, 486, 15920 - 486, 11802)
pvalue_nonfixe = phyper(920 - 1, 1389, 17166 - 1389, 11794)
presence = c(745,11057)
absence = c(0,4118)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me1_fixe_rep = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me1_fixe_rep)
presence = c(920,10874)
absence = c(469,3453)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me1_nonfixe_rep = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me1_nonfixe_rep)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 0.0182405
La pvalue du test de fisher pour les motifs fixé est de 3.317013410^{-100} Celle du test de fisher pour les motifs non fixé est de 1.431330110^{-14}`
total_svbF7_unbound = 920 + 469
total_svbF7_bound = 745 + 0
percent_svbf7_H3K4me1_unbound = round(100 * 920 / total_svbF7_unbound, 2 )
percent_svbf7_unbound_without_H3K4me1 = round(100 * 469 / total_svbF7_unbound, 2 )
percent_svbf7_H3K4me1_bound = round(100 * 746 / total_svbF7_bound, 2 )
percent_svbf7_bound_without_H3K4me1 = round(100 * 0 / total_svbF7_bound, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me1_absent = c(percent_svbf7_bound_without_H3K4me1,percent_svbf7_unbound_without_H3K4me1)
H3K4me1_present = c(percent_svbf7_H3K4me1_bound,percent_svbf7_H3K4me1_unbound)
data_H3K4me1_rep = data.frame(etat_svb,H3K4me1_absent,H3K4me1_present)
datatable(data_H3K4me1_rep,rownames = F,filter = "none", colnames = c("Regions without H3K4me1","Regions with H3K4me1" ))
fig3 = plot_ly(data_H3K4me1_rep, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig3 = fig3 %>% add_trace(y = ~H3K4me1_absent, name = "H3K4me1 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb (Rep condition)", barmode = "stack")
fig3
fig3 = plot_ly(data_H3K4me1_rep, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig3 = fig3 %>% add_trace(y = ~H3K4me1_absent, name = "H3K4me1 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb (Rep condition)")
fig3
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 unbound | 721 | 668 |
| absent svbF7 unbound | 9924 | 6743 |
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 bound | 405 | 81 |
| absent svbF7 bound | 10240 | 7598 |
pvalue_fixe = phyper(405 - 1, 486, 18324 - 486, 10645)
pvalue_nonfixe = phyper(721 - 1, 1389, 18025 - 1389, 10645)
presence = c(405,81)
absence = c(10240,7598)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me3_fixe_ctrl = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me3_fixe_ctrl)
presence = c(721,9924)
absence = c(668,6743)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me3_nonfixe_ctrl = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me3_nonfixe_ctrl)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 8.857963910^{-9}
La pvalue du test de fisher pour les motifs fixé est de 2.206021510^{-33} Celle du test de fisher pour les motifs non fixé est de 3.492107710^{-8}`
total_svbF7_unbound_H3K4me3 = 721 + 668
total_svbF7_bound_H3K4me3 = 405 + 81
percent_svbf7_H3K4me3_unbound = round(100 * 721 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_unbound_without_H3K4me3 = round(100 * 668 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_H3K4me3_bound = round(100 * 405 / total_svbF7_bound_H3K4me3, 2 )
percent_svbf7_bound_without_H3K4me3 = round(100 * 81 / total_svbF7_bound_H3K4me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me3_absent = c(percent_svbf7_bound_without_H3K4me3,percent_svbf7_unbound_without_H3K4me3)
H3K4me3_present = c(percent_svbf7_H3K4me3_bound,percent_svbf7_H3K4me3_unbound)
data_H3K4me3_ctrl = data.frame(etat_svb,H3K4me3_absent,H3K4me3_present)
datatable(data_H3K4me3_ctrl,rownames = F,filter = "none",colnames = c("Regions without H3K4me3","Regions with H3K4me3" ))
fig4 = plot_ly(data_H3K4me3_ctrl, x = ~etat_svb,y = ~H3K4me3_absent, type = "bar",name = "H3K4me3 absent", color = I("grey"))
fig4 = fig4 %>% add_trace(y = ~H3K4me3_present, name = "H3K4me3 present", color = I("pink"))
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb (Ctrl condition)", barmode = "stack")
fig4
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 unbound | 343 | 1046 |
| absent svbF7 unbound | 6896 | 9899 |
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 bound | 334 | 152 |
| absent svbF7 bound | 6906 | 11030 |
pvalue_fixe = phyper(334 - 1, 486, 18422 - 486, 7240)
pvalue_nonfixe = phyper(343 - 1, 1389, 18151 - 1389, 7239)
presence = c(334,6906)
absence = c(152,11030)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me3_fixe_act = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me3_fixe_act)
presence = c(343,6896)
absence = c(1046,9899)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me3_nonfixe_act = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me3_nonfixe_act)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 1.091793410^{-35}
La pvalue du test de fisher pour les motifs fixé est de 4.034298210^{-40} Celle du test de fisher pour les motifs non fixé est de 8.501713810^{-35}`
total_svbF7_unbound_H3K4me3 = 343 + 1046
total_svbF7_bound_H3K4me3 = 334 + 152
percent_svbf7_H3K4me3_unbound = round(100 * 343 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_unbound_without_H3K4me3 = round(100 * 1046 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_H3K4me3_bound = round(100 * 334 / total_svbF7_bound_H3K4me3, 2 )
percent_svbf7_bound_without_H3K4me3 = round(100 * 152 / total_svbF7_bound_H3K4me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me3_absent = c(percent_svbf7_bound_without_H3K4me3,percent_svbf7_unbound_without_H3K4me3)
H3K4me3_present = c(percent_svbf7_H3K4me3_bound,percent_svbf7_H3K4me3_unbound)
data_H3K4me3_act = data.frame(etat_svb,H3K4me3_absent,H3K4me3_present)
datatable(data_H3K4me3_act,rownames = F,filter = "none",colnames = c("Regions without H3K4me3","Regions with H3K4me3" ))
fig4 = plot_ly(data_H3K4me3_act, x = ~etat_svb,y = ~H3K4me3_present, type = "bar",name = "H3K4me3 present", color = I("pink"))
fig4 = fig4 %>% add_trace(y = ~H3K4me3_absent, name = "H3K4me3 absent", color = I("grey"))
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb (Act condition)", barmode = "stack")
fig4
fig4 = plot_ly(data_H3K4me3_act, x = ~etat_svb,y = ~H3K4me3_present, type = "bar",name = "H3K4me3 present", color = I("pink"))
fig4 = fig4 %>% add_trace(y = ~H3K4me3_absent, name = "H3K4me3 absent", color = I("grey"))
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb (Act condition)")
fig4
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 unbound | 146 | 1243 |
| absent svbF7 unbound | 4548 | 10940 |
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 bound | 328 | 158 |
| absent svbF7 bound | 4467 | 12262 |
pvalue_fixe = phyper(328 - 1, 486, 17215 - 486, 4795)
pvalue_nonfixe = phyper(328 - 1, 1389, 18685 - 1389, 11861)
presence = c(328,4467)
absence = c(158,12262)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me3_fixe_rep = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me3_fixe_rep)
presence = c(328,4467)
absence = c(158,12262)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me3_nonfixe_rep = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me3_nonfixe_rep)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 5.097738610^{-219}
La pvalue du test de fisher pour les motifs fixé est de 7.836987810^{-76} Celle du test de fisher pour les motifs non fixé est de 7.836987810^{-76}`
total_svbF7_unbound_H3K4me3 = 146 + 1243
total_svbF7_bound_H3K4me3 = 328 + 158
percent_svbf7_H3K4me3_unbound = round(100 * 146 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_unbound_without_H3K4me3 = round(100 * 1243 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_H3K4me3_bound = round(100 * 328 / total_svbF7_bound_H3K4me3, 2 )
percent_svbf7_bound_without_H3K4me3 = round(100 * 158 / total_svbF7_bound_H3K4me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me3_absent = c(percent_svbf7_bound_without_H3K4me3,percent_svbf7_unbound_without_H3K4me3)
H3K4me3_present = c(percent_svbf7_H3K4me3_bound,percent_svbf7_H3K4me3_unbound)
data_H3K4me3_rep = data.frame(etat_svb,H3K4me3_absent,H3K4me3_present)
datatable(data_H3K4me3_rep,rownames = F,filter = "none",colnames = c("Regions without H3K4me3","Regions with H3K4me3" ))
fig4 = plot_ly(data_H3K4me3_rep, x = ~etat_svb,y = ~H3K4me3_present, type = "bar",name = "H3K4me3 present", color = I("pink"))
fig4 = fig4 %>% add_trace(y = ~H3K4me3_absent, name = "H3K4me3 absent", color = I("grey"))
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb (Rep condition)", barmode = "stack")
fig4
fig4 = plot_ly(data_H3K4me3_rep, x = ~etat_svb,y = ~H3K4me3_present, type = "bar",name = "H3K4me3 present", color = I("pink"))
fig4 = fig4 %>% add_trace(y = ~H3K4me3_absent, name = "H3K4me3 absent", color = I("grey"))
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb (Rep condition)")
fig4
total_K4me1_S2 = 8782
total_K4me3_S2 = 4812
rapp_fixe = round((contingence_H3K4me1_fixe_ctrl[1,1] / total_K4me1_S2 ) / (contingence_H3K4me3_fixe_ctrl[1,1] / total_K4me3_S2),2)
rapp_nonfixe = round((contingence_H3K4me1_nonfixe_ctrl[1,1] / total_K4me1_S2) / (contingence_H3K4me3_nonfixe_ctrl[1,1] / total_K4me3_S2) ,2)
Il y a 0.94 fois de H3K4me1 que de H3K4me3 fixé.
Il y a 0.62 fois de H3K4me1 que de H3K4me3 non fixé.
total_K4me1_S2 = 8782
total_K4me3_S2 = 4812
rapp_fixe = round((contingence_H3K4me1_fixe_act [1,1] / total_K4me1_S2 ) / (contingence_H3K4me3_fixe_act[1,1] / total_K4me3_S2),2)
rapp_nonfixe = round((contingence_H3K4me1_nonfixe_act[1,1] / total_K4me1_S2) / (contingence_H3K4me3_nonfixe_act[1,1] / total_K4me3_S2) ,2)
Il y a 1.24 fois de H3K4me1 que de H3K4me3 fixé.
Il y a 1.58 fois de H3K4me1 que de H3K4me3 non fixé.
total_K4me1_S2 = 8782
total_K4me3_S2 = 4812
rapp_fixe = round((contingence_H3K4me1_fixe_rep[1,1] / total_K4me1_S2 ) / (contingence_H3K4me3_fixe_rep[1,1] / total_K4me3_S2),2)
rapp_nonfixe = round((contingence_H3K4me1_nonfixe_rep[1,1] / total_K4me1_S2) / (contingence_H3K4me3_nonfixe_rep[1,1] / total_K4me3_S2) ,2)
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 unbound | 213 | 1176 |
| absent svbF7 unbound | 5418 | 9019 |
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 bound | 446 | 40 |
| absent svbF7 bound | 5189 | 10357 |
pvalue_fixe = phyper(446 - 1, 486, 16032 - 486, 5635)
pvalue_nonfixe = phyper(213 - 1, 1389, 15826 - 1389, 5631)
presence = c(446,5189)
absence = c(40,10357)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27ac_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27ac_fixe)
presence = c(213,5418)
absence = c(1176,9019)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27ac_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27ac_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 1.789608210^{-69}
La pvalue du test de fisher pour les motifs fixé est de 1.388775210^{-156} Celle du test de fisher pour les motifs non fixé est de 9.597761510^{-69}`
total_svbF7_unbound_H3K27ac = 213 + 1176
total_svbF7_bound_H3K27ac = 446 + 40
percent_svbf7_H3K27ac_unbound = round(100 * 213 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_unbound_without_H3K27ac = round(100 * 1176 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_H3K27ac_bound = round(100 * 446 / total_svbF7_bound_H3K27ac, 2 )
percent_svbf7_bound_without_H3K27ac = round(100 * 40 / total_svbF7_bound_H3K27ac, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K27ac_absent = c(percent_svbf7_bound_without_H3K27ac,percent_svbf7_unbound_without_H3K27ac)
H3K27ac_present = c(percent_svbf7_H3K27ac_bound,percent_svbf7_H3K27ac_unbound)
data_H3K27ac_ctrl = data.frame(etat_svb,H3K27ac_absent,H3K27ac_present)
datatable(data_H3K27ac_ctrl,rownames = F,filter = "none",colnames = c("Regions without H3K27ac","Regions with H3K27ac" ))
fig1 = plot_ly(data_H3K27ac_ctrl, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig1 = fig1 %>% add_trace(y = ~H3K27ac_absent, name = "H3K27ac absent", color = I("grey"))
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb ( Ctrl condition)", barmode = "stack")
fig1
fig1 = plot_ly(data_H3K27ac_ctrl, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig1 = fig1 %>% add_trace(y = ~H3K27ac_absent, name = "H3K27ac absent", color = I("grey"))
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb ( Ctrl condition)")
fig1
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 unbound | 206 | 1183 |
| absent svbF7 unbound | 5471 | 9125 |
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 bound | 445 | 41 |
| absent svbF7 bound | 5236 | 10473 |
pvalue_fixe = phyper(445 - 1, 486, 166195 - 486, 5681)
pvalue_nonfixe = phyper(206 - 1, 1389, 15985 - 1389, 5677)
presence = c(445,5236)
absence = c(41,10473)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27ac_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27ac_fixe)
presence = c(206,5471)
absence = c(1183,9125)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27ac_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27ac_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 9.47918510^{-73}
La pvalue du test de fisher pour les motifs fixé est de 1.405424510^{-155} Celle du test de fisher pour les motifs non fixé est de 4.607645810^{-72}`
total_svbF7_unbound_H3K27ac = 206 + 1183
total_svbF7_bound_H3K27ac = 445 + 41
percent_svbf7_H3K27ac_unbound = round(100 * 206 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_unbound_without_H3K27ac = round(100 * 1183 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_H3K27ac_bound = round(100 * 445 / total_svbF7_bound_H3K27ac, 2 )
percent_svbf7_bound_without_H3K27ac = round(100 * 41 / total_svbF7_bound_H3K27ac, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K27ac_absent = c(percent_svbf7_bound_without_H3K27ac,percent_svbf7_unbound_without_H3K27ac)
H3K27ac_present = c(percent_svbf7_H3K27ac_bound,percent_svbf7_H3K27ac_unbound)
data_H3K27ac_act = data.frame(etat_svb,H3K27ac_absent,H3K27ac_present)
datatable(data_H3K27ac_act,rownames = F,filter = "none",colnames = c("Regions without H3K27ac","Regions with H3K27ac" ))
fig1 = plot_ly(data_H3K27ac_act, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig1 = fig1 %>% add_trace(y = ~H3K27ac_absent, name = "H3K27ac absent", color = I("grey"))
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb ( Act Condtion) ", barmode = "stack")
fig1
fig1 = plot_ly(data_H3K27ac_act, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig1 = fig1 %>% add_trace(y = ~H3K27ac_absent, name = "H3K27ac absent", color = I("grey"))
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb ( Act Condtion) ")
fig1
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 unbound | 206 | 1183 |
| absent svbF7 unbound | 5425 | 9033 |
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 bound | 440 | 46 |
| absent svbF7 bound | 5294 | 10374 |
pvalue_fixe = phyper(440 - 1, 486, 16054 - 486, 5634)
pvalue_nonfixe = phyper(106 - 1, 1389, 15847 - 1389, 5631)
presence = c(440,5294)
absence = c(46,10374)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27ac_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27ac_fixe)
presence = c(206,5425)
absence = c(1183,9033)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27ac_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27ac_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 3.024282210^{-142}
La pvalue du test de fisher pour les motifs fixé est de 7.595208310^{-147} Celle du test de fisher pour les motifs non fixé est de 3.794733510^{-72}`
total_svbF7_unbound_H3K27ac = 206 + 1183
total_svbF7_bound_H3K27ac = 440 + 46
percent_svbf7_H3K27ac_unbound = round(100 * 206 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_unbound_without_H3K27ac = round(100 * 1183 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_H3K27ac_bound = round(100 * 440 / total_svbF7_bound_H3K27ac, 2 )
percent_svbf7_bound_without_H3K27ac = round(100 * 46 / total_svbF7_bound_H3K27ac, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K27ac_absent = c(percent_svbf7_bound_without_H3K27ac,percent_svbf7_unbound_without_H3K27ac)
H3K27ac_present = c(percent_svbf7_H3K27ac_bound,percent_svbf7_H3K27ac_unbound)
data_H3K27ac_rep = data.frame(etat_svb,H3K27ac_absent,H3K27ac_present)
datatable(data_H3K27ac_rep,rownames = F,filter = "none",colnames = c("Regions without H3K27ac","Regions with H3K27ac" ))
fig1 = plot_ly(data_H3K27ac_rep, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig1 = fig1 %>% add_trace(y = ~H3K27ac_absent, name = "H3K27ac absent", color = I("grey"))
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb ( Rep condition) ", barmode = "stack")
fig1
fig1 = plot_ly(data_H3K27ac_rep, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig1 = fig1 %>% add_trace(y = ~H3K27ac_absent, name = "H3K27ac absent", color = I("grey"))
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb ( Rep condition) ")
fig1
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 unbound | 1928 | 0 |
| absent svbF7 unbound | 13199 | 0 |
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 bound | 410 | 76 |
| absent svbF7 bound | 14717 | 87 |
pvalue_fixe = phyper(410 - 1, 486, 15290 - 486, 15127)
pvalue_nonfixe = phyper(1928 - 1, 1389, 15127 - 1389, 15127)
presence = c(410,14717)
absence = c(76,87)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27me3_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27me3_fixe)
presence = c(1928,13199)
absence = c(0,0)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27me3_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27me3_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 5.489481710^{-72} Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 1.745591210^{-70} Celle du test de fisher pour les motifs non fixé est de 1`
total_svbF7_unbound_H3K27me3 = 1928 + 0
total_svbF7_bound_H3K27me3 = 410 + 76
percent_svbf7_H3K27me3_unbound = round(100 * 1928 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_unbound_without_H3K27me3 = round(100 * 0 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_H3K27me3_bound = round(100 * 410 / total_svbF7_bound_H3K27me3, 2 )
percent_svbf7_bound_without_H3K27me3 = round(100 * 76 / total_svbF7_bound_H3K27me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K27me3_absent = c(percent_svbf7_bound_without_H3K27me3,percent_svbf7_unbound_without_H3K27me3)
H3K27me3_present = c(percent_svbf7_H3K27me3_bound,percent_svbf7_H3K27me3_unbound)
data_H3K27me3_ctrl = data.frame(etat_svb,H3K27me3_absent,H3K27me3_present)
datatable(data_H3K27me3_ctrl,rownames = F,filter = "none",colnames = c("Regions without H3K27me3","Regions with H3K27me3" ))
fig2 = plot_ly(data_H3K27me3_ctrl, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color =I("purple"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_absent, name = "H3K27me3 absent",color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb (Ctrl condition)", barmode = "stack")
fig2
fig2 = plot_ly(data_H3K27me3_ctrl, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color =I("purple"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_absent, name = "H3K27me3 absent",color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb (Ctrl condition)")
fig2
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 unbound | 1863 | 0 |
| absent svbF7 unbound | 12446 | 119 |
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 bound | 410 | 76 |
| absent svbF7 bound | 14717 | 87 |
pvalue_fixe = phyper(410 - 1, 486, 15290 - 486, 15127)
pvalue_nonfixe = phyper(1863 - 1, 1389, 14428 - 1389, 14309)
presence = c(410,14717)
absence = c(76,87)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27me3_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27me3_fixe)
presence = c(1863,12446)
absence = c(0,119)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27me3_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27me3_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 5.489481710^{-72} Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 1.745591210^{-70} Celle du test de fisher pour les motifs non fixé est de 1.176369110^{-7}`
total_svbF7_unbound_H3K27me3 = 1863+ 0
total_svbF7_bound_H3K27me3 = 410 + 76
percent_svbf7_H3K27me3_unbound = round(100 * 1863 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_unbound_without_H3K27me3 = round(100 * 0 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_H3K27me3_bound = round(100 * 410 / total_svbF7_bound_H3K27me3, 2 )
percent_svbf7_bound_without_H3K27me3 = round(100 * 76 / total_svbF7_bound_H3K27me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K27me3_absent = c(percent_svbf7_bound_without_H3K27me3,percent_svbf7_unbound_without_H3K27me3)
H3K27me3_present = c(percent_svbf7_H3K27me3_bound,percent_svbf7_H3K27me3_unbound)
data_H3K27me3_act = data.frame(etat_svb,H3K27me3_absent,H3K27me3_present)
datatable(data_H3K27me3_act,rownames = F,filter = "none",colnames = c("Regions without H3K27me3","Regions with H3K27me3" ))
fig2 = plot_ly(data_H3K27me3_act, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color =I("purple"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_present, name = "H3K27me3 absent",color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb ( Act condition ) ", barmode = "stack")
fig2
fig2 = plot_ly(data_H3K27me3_act, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color =I("purple"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_present, name = "H3K27me3 absent",color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb ( Act condition ) ")
fig2
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 unbound | 1878 | 0 |
| absent svbF7 unbound | 13423 | 0 |
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 bound | 452 | 34 |
| absent svbF7 bound | 14849 | 0 |
pvalue_fixe = phyper(452 - 1, 486, 15335 - 486, 15301)
pvalue_nonfixe = phyper(1878 - 1, 1389, 15301 - 1389, 15301)
presence = c(452,14849)
absence = c(34,0)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27me3_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27me3_fixe)
presence = c(1878,13423)
absence = c(0,0)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27me3_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27me3_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 0 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 3.427962810^{-52} Celle du test de fisher pour les motifs non fixé est de 1`
total_svbF7_unbound_H3K27me3 = 1878+ 0
total_svbF7_bound_H3K27me3 = 452 + 34
percent_svbf7_H3K27me3_unbound = round(100 * 1878 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_unbound_without_H3K27me3 = round(100 * 0 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_H3K27me3_bound = round(100 * 452 / total_svbF7_bound_H3K27me3, 2 )
percent_svbf7_bound_without_H3K27me3 = round(100 * 34 / total_svbF7_bound_H3K27me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K27me3_absent = c(percent_svbf7_bound_without_H3K27me3,percent_svbf7_unbound_without_H3K27me3)
H3K27me3_present = c(percent_svbf7_H3K27me3_bound,percent_svbf7_H3K27me3_unbound)
data_H3K27me3_rep = data.frame(etat_svb,H3K27me3_absent,H3K27me3_present)
datatable(data_H3K27me3_rep,rownames = F,filter = "none",colnames = c("Regions without H3K27me3","Regions with H3K27me3" ))
fig2 = plot_ly(data_H3K27me3_rep, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color =I("purple"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_absent, name = "H3K27me3 absent",color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb ( Rep condition ) ", barmode = "stack")
fig2
fig2 = plot_ly(data_H3K27me3_rep, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color =I("purple"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_absent, name = "H3K27me3 absent",color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb ( Rep condition ) ")
fig2
Je regarde ici l’enrichisement en histones des motifs de Svb en présence des différentes formes de Svb ( Act/ Rep) et Ctrl sur les pics associés aux gènes cibles directes
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 unbound | 1415 | 372 |
| absent svbF7 unbound | 8771 | 4422 |
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 bound | 67 | 0 |
| absent svbF7 bound | 10129 | 5142 |
pvalue_fixe = phyper(67 - 1, 45, 15338 - 45, 10196)
pvalue_nonfixe = phyper(1415 - 1, 1787, 14980 - 1787, 10186)
presence = c(67,10129)
absence = c(0,5142)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me1_fixe_ctrl = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me1_fixe_ctrl)
presence = c(1415,8771)
absence = c(372,4422)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me1_nonfixe_ctrl = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me1_nonfixe_ctrl)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 2.286749710^{-12} Celle du test de fisher pour les motifs non fixé est de 6.388705810^{-29}`
total_svbF7_unbound = 1415 + 372
total_svbF7_bound = 67 + 0
percent_svbf7_H3K4me1_unbound = round(100 * 1415 / total_svbF7_unbound, 2 )
percent_svbf7_unbound_without_H3K4me1 = round(100 * 372 / total_svbF7_unbound, 2 )
percent_svbf7_H3K4me1_bound = round(100 * 67 / total_svbF7_bound, 2 )
percent_svbf7_bound_without_H3K4me1 = round(100 * 0 / total_svbF7_bound, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me1_absent = c(percent_svbf7_bound_without_H3K4me1,percent_svbf7_unbound_without_H3K4me1)
H3K4me1_present = c(percent_svbf7_H3K4me1_bound,percent_svbf7_H3K4me1_unbound)
data_H3K4me1_ctrl = data.frame(etat_svb,H3K4me1_absent,H3K4me1_present)
datatable(data_H3K4me1_ctrl,rownames = F,filter = "none", colnames = c("Regions without H3K4me1","Regions with H3K4me1" ))
fig3 = plot_ly(data_H3K4me1_ctrl, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig3 = fig3 %>% add_trace(y = ~H3K4me1_absent, name = "H3K4me1 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb (Ctrl condition)", barmode = "stack")
fig3
fig3 = plot_ly(data_H3K4me1_ctrl, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig3 = fig3 %>% add_trace(y = ~H3K4me1_absent, name = "H3K4me1 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb (Ctrl condition)")
fig3
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 unbound | 1637 | 150 |
| absent svbF7 unbound | 10600 | 3396 |
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 bound | 69 | 0 |
| absent svbF7 bound | 12181 | 3930 |
pvalue_fixe = phyper(68 - 1, 45, 16180 -45, 12250)
pvalue_nonfixe = phyper(1637 - 1, 1787, 15783 - 1787, 12237)
presence = c(60,12181)
absence = c(0,3930)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me1_fixe_act = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me1_fixe_act)
presence = c(1637,10600)
absence = c(150,3396)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me1_nonfixe_act = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me1_nonfixe_act)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 7.216512910^{-8} Celle du test de fisher pour les motifs non fixé est de 1.09857510^{-61}`
total_svbF7_unbound = 1637 + 150
total_svbF7_bound = 69 + 0
percent_svbf7_H3K4me1_unbound = round(100 * 1637 / total_svbF7_unbound, 2 )
percent_svbf7_unbound_without_H3K4me1 = round(100 * 150 / total_svbF7_unbound, 2 )
percent_svbf7_H3K4me1_bound = round(100 * 69 / total_svbF7_bound, 2 )
percent_svbf7_bound_without_H3K4me1 = round(100 * 0 / total_svbF7_bound, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me1_absent = c(percent_svbf7_bound_without_H3K4me1,percent_svbf7_unbound_without_H3K4me1)
H3K4me1_present = c(percent_svbf7_H3K4me1_bound,percent_svbf7_H3K4me1_unbound)
data_H3K4me1_act = data.frame(etat_svb,H3K4me1_absent,H3K4me1_present)
datatable(data_H3K4me1_act,rownames = F,filter = "none", colnames = c("Regions without H3K4me1","Regions with H3K4me1" ))
fig3 = plot_ly(data_H3K4me1_act, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig3 = fig3 %>% add_trace(y = ~H3K4me1_absent, name = "H3K4me1 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb (Act condition)", barmode = "stack")
fig3
fig3 = plot_ly(data_H3K4me1_act, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig3 = fig3 %>% add_trace(y = ~H3K4me1_absent, name = "H3K4me1 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb (Act condition)")
fig3
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 unbound | 1563 | 224 |
| absent svbF7 unbound | 10231 | 3579 |
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 unbound | 65 | 0 |
| absent svbF7 unbound | 11737 | 4182 |
pvalue_fixe = phyper(65 - 1, 45, 15984 - 45, 11802)
pvalue_nonfixe = phyper(1563 - 1, 1787, 15597 - 1787, 11794)
presence = c(65,11737)
absence = c(0,4182)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me1_fixe_rep = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me1_fixe_rep)
presence = c(1563,10231)
absence = c(224,3579)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me1_nonfixe_rep = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me1_nonfixe_rep)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 4.59151510^{-9} Celle du test de fisher pour les motifs non fixé est de 1.23021910^{-39}`
total_svbF7_unbound = 1563 + 224
total_svbF7_bound = 65 + 0
percent_svbf7_H3K4me1_unbound = round(100 * 1563 / total_svbF7_unbound, 2 )
percent_svbf7_unbound_without_H3K4me1 = round(100 * 224 / total_svbF7_unbound, 2 )
percent_svbf7_H3K4me1_bound = round(100 * 65 / total_svbF7_bound, 2 )
percent_svbf7_bound_without_H3K4me1 = round(100 * 0 / total_svbF7_bound, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me1_absent = c(percent_svbf7_bound_without_H3K4me1,percent_svbf7_unbound_without_H3K4me1)
H3K4me1_present = c(percent_svbf7_H3K4me1_bound,percent_svbf7_H3K4me1_unbound)
data_H3K4me1_rep = data.frame(etat_svb,H3K4me1_absent,H3K4me1_present)
datatable(data_H3K4me1_rep,rownames = F,filter = "none", colnames = c("Regions without H3K4me1","Regions with H3K4me1" ))
fig3 = plot_ly(data_H3K4me1_rep, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig3 = fig3 %>% add_trace(y = ~H3K4me1_absent, name = "H3K4me1 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb (Rep condition)", barmode = "stack")
fig3
fig3 = plot_ly(data_H3K4me1_rep, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig3 = fig3 %>% add_trace(y = ~H3K4me1_absent, name = "H3K4me1 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb (Rep condition)")
fig3
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 unbound | 1080 | 707 |
| absent svbF7 unbound | 9565 | 6548 |
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 bound | 33 | 12 |
| absent svbF7 bound | 10612 | 7753 |
pvalue_fixe = phyper(33 - 1, 45, 18410 - 45, 10645)
pvalue_nonfixe = phyper(1080 - 1, 1787, 17900 - 1787, 10645)
presence = c(33,10612)
absence = c(12,7753)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me3_fixe_ctrl = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me3_fixe_ctrl)
presence = c(1080,956)
absence = c(707,6548)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me3_nonfixe_ctrl = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me3_nonfixe_ctrl)
La pvalue du test de hypergéométrique pour les motifs fixé est de 0.9768974 Celle du test de hypergéométrique pour les motifs non fixé est de 0.8028997
La pvalue du test de fisher pour les motifs fixé est de 0.0350842 Celle du test de fisher pour les motifs non fixé est de 0`
total_svbF7_unbound_H3K4me3 = 1080 + 707
total_svbF7_bound_H3K4me3 = 33 + 12
percent_svbf7_H3K4me3_unbound = round(100 * 1080 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_unbound_without_H3K4me3 = round(100 * 707 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_H3K4me3_bound = round(100 * 33 / total_svbF7_bound_H3K4me3, 2 )
percent_svbf7_bound_without_H3K4me3 = round(100 * 12 / total_svbF7_bound_H3K4me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me3_absent = c(percent_svbf7_bound_without_H3K4me3,percent_svbf7_unbound_without_H3K4me3)
H3K4me3_present = c(percent_svbf7_H3K4me3_bound,percent_svbf7_H3K4me3_unbound)
data_H3K4me3_ctrl = data.frame(etat_svb,H3K4me3_absent,H3K4me3_present)
datatable(data_H3K4me3_ctrl,rownames = F,filter = "none",colnames = c("Regions without H3K4me3","Regions with H3K4me3" ))
fig4 = plot_ly(data_H3K4me3_ctrl, x = ~etat_svb,y = ~H3K4me3_present, type = "bar",name = "H3K4me3 present", color = I("pink"))
fig4 = fig4 %>% add_trace(y = ~H3K4me3_absent, name = "H3K4me3 absent", color = I("grey"))
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb (Ctrl condition)", barmode = "stack")
fig4
fig4 = plot_ly(data_H3K4me3_ctrl, x = ~etat_svb,y = ~H3K4me3_present, type = "bar",name = "H3K4me3 present", color = I("pink"))
fig4 = fig4 %>% add_trace(y = ~H3K4me3_absent, name = "H3K4me3 absent", color = I("grey"))
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb (Ctrl condition)")
fig4
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 unbound | 638 | 1149 |
| absent svbF7 unbound | 6601 | 9605 |
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 bound | 33 | 12 |
| absent svbF7 bound | 7207 | 11257 |
pvalue_fixe = phyper(33 - 1, 45, 18509 - 45, 7240)
pvalue_nonfixe = phyper(638 - 1, 1787, 17993 - 1787, 7239)
presence = c(33,7207)
absence = c(12,11257)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me3_fixe_act = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me3_fixe_act)
presence = c(638,6601)
absence = c(1149,9605)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me3_nonfixe_act = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me3_nonfixe_act)
La pvalue du test de hypergéométrique pour les motifs fixé est de 0.9999967 Celle du test de hypergéométrique pour les motifs non fixé est de 1.558858610^{-5}
La pvalue du test de fisher pour les motifs fixé est de 4.11252610^{-6} Celle du test de fisher pour les motifs non fixé est de 3.792336310^{-5}`
total_svbF7_unbound_H3K4me3 = 638 + 1149
total_svbF7_bound_H3K4me3 = 33 + 12
percent_svbf7_H3K4me3_unbound = round(100 * 638 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_unbound_without_H3K4me3 = round(100 * 1149 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_H3K4me3_bound = round(100 * 33 / total_svbF7_bound_H3K4me3, 2 )
percent_svbf7_bound_without_H3K4me3 = round(100 * 12 / total_svbF7_bound_H3K4me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me3_absent = c(percent_svbf7_bound_without_H3K4me3,percent_svbf7_unbound_without_H3K4me3)
H3K4me3_present = c(percent_svbf7_H3K4me3_bound,percent_svbf7_H3K4me3_unbound)
data_H3K4me3_act = data.frame(etat_svb,H3K4me3_absent,H3K4me3_present)
datatable(data_H3K4me3_act,rownames = F,filter = "none",colnames = c("Regions without H3K4me3","Regions with H3K4me3" ))
fig4 = plot_ly(data_H3K4me3_act, x = ~etat_svb,y = ~H3K4me3_present, type = "bar",name = "H3K4me3 present", color = I("pink"))
fig4 = fig4 %>% add_trace(y = ~H3K4me3_absent, name = "H3K4me3 absent", color = I("grey"))
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb (Act condition)", barmode = "stack")
fig4
fig4 = plot_ly(data_H3K4me3_act, x = ~etat_svb,y = ~H3K4me3_present, type = "bar",name = "H3K4me3 present", color = I("pink"))
fig4 = fig4 %>% add_trace(y = ~H3K4me3_absent, name = "H3K4me3 absent", color = I("grey"))
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb (Act condition)")
fig4
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 unbound | 1263 | 524 |
| absent svbF7 unbound | 10598 | 6133 |
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 bound | 32 | 13 |
| absent svbF7 bound | 4763 | 12483 |
pvalue_fixe = phyper(32 - 1, 45, 17291 - 45, 4795)
pvalue_nonfixe = phyper(1263 - 1, 1787, 18518 - 1787, 11861)
presence = c(32,4763)
absence = c(13,12483)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me3_fixe_rep = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me3_fixe_rep)
presence = c(1263,524)
absence = c(10598,6133 )
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me3_nonfixe_rep = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me3_nonfixe_rep)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 1.783416710^{-9} Celle du test de fisher pour les motifs non fixé est de 5.398360210^{-10}`
total_svbF7_unbound_H3K4me3 = 1263 + 524
total_svbF7_bound_H3K4me3 = 32 + 13
percent_svbf7_H3K4me3_unbound = round(100 * 1263 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_unbound_without_H3K4me3 = round(100 * 524 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_H3K4me3_bound = round(100 * 32 / total_svbF7_bound_H3K4me3, 2 )
percent_svbf7_bound_without_H3K4me3 = round(100 * 13 / total_svbF7_bound_H3K4me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me3_absent = c(percent_svbf7_bound_without_H3K4me3,percent_svbf7_unbound_without_H3K4me3)
H3K4me3_present = c(percent_svbf7_H3K4me3_bound,percent_svbf7_H3K4me3_unbound)
data_H3K4me3_rep = data.frame(etat_svb,H3K4me3_absent,H3K4me3_present)
datatable(data_H3K4me3_rep,rownames = F,filter = "none",colnames = c("Regions without H3K4me3","Regions with H3K4me3" ))
fig4 = plot_ly(data_H3K4me3_rep, x = ~etat_svb,y = ~H3K4me3_present, type = "bar",name = "H3K4me3 present", color = I("pink"))
fig4 = fig4 %>% add_trace(y = ~H3K4me3_absent, name = "H3K4me3 absent", color = I("grey"))
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb (Rep condition)", barmode = "stack")
fig4
fig4 = plot_ly(data_H3K4me3_rep, x = ~etat_svb,y = ~H3K4me3_present, type = "bar",name = "H3K4me3 present", color = I("pink"))
fig4 = fig4 %>% add_trace(y = ~H3K4me3_absent, name = "H3K4me3 absent", color = I("grey"))
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb (Rep condition)")
fig4
total_K4me1_S2 = 8782
total_K4me3_S2 = 4812
rapp_fixe = round((contingence_H3K4me1_fixe_ctrl[1,1] / total_K4me1_S2 ) / (contingence_H3K4me3_fixe_ctrl[1,1] / total_K4me3_S2),2)
rapp_nonfixe = round((contingence_H3K4me1_nonfixe_ctrl[1,1] / total_K4me1_S2) / (contingence_H3K4me3_nonfixe_ctrl[1,1] / total_K4me3_S2) ,2)
Il y a 1.11 fois de H3K4me1 que de H3K4me3 fixé.
Il y a 0.72 fois de H3K4me1 que de H3K4me3 non fixé.
total_K4me1_S2 = 8782
total_K4me3_S2 = 4812
rapp_fixe = round((contingence_H3K4me1_fixe_act [1,1] / total_K4me1_S2 ) / (contingence_H3K4me3_fixe_act[1,1] / total_K4me3_S2),2)
rapp_nonfixe = round((contingence_H3K4me1_nonfixe_act[1,1] / total_K4me1_S2) / (contingence_H3K4me3_nonfixe_act[1,1] / total_K4me3_S2) ,2)
Il y a 1 fois de H3K4me1 que de H3K4me3 fixé.
Il y a 1.41 fois de H3K4me1 que de H3K4me3 non fixé.
total_K4me1_S2 = 8782
total_K4me3_S2 = 4812
rapp_fixe = round((contingence_H3K4me1_fixe_rep[1,1] / total_K4me1_S2 ) / (contingence_H3K4me3_fixe_rep[1,1] / total_K4me3_S2),2)
rapp_nonfixe = round((contingence_H3K4me1_nonfixe_rep[1,1] / total_K4me1_S2) / (contingence_H3K4me3_nonfixe_rep[1,1] / total_K4me3_S2) ,2)
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 unbound | 602 | 1185 |
| absent svbF7 unbound | 5029 | 8890 |
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 bound | 43 | 2 |
| absent svbF7 bound | 5592 | 10461 |
pvalue_fixe = phyper(43 - 1, 45, 16098 - 45, 5635)
pvalue_nonfixe = phyper(602 - 1, 1787, 15706 - 1787, 5631)
presence = c(43,5592)
absence = c(2,10461)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27ac_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27ac_fixe)
presence = c(602,5029)
absence = c(1185,8890)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27ac_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27ac_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 0.019714
La pvalue du test de fisher pour les motifs fixé est de 9.685414710^{-18} Celle du test de fisher pour les motifs non fixé est de 0.0436541`
total_svbF7_unbound_H3K27ac = 602 + 1185
total_svbF7_bound_H3K27ac = 43 + 2
percent_svbf7_H3K27ac_unbound = round(100 * 602 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_unbound_without_H3K27ac = round(100 * 1185 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_H3K27ac_bound = round(100 * 43 / total_svbF7_bound_H3K27ac, 2 )
percent_svbf7_bound_without_H3K27ac = round(100 * 2 / total_svbF7_bound_H3K27ac, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K27ac_absent = c(percent_svbf7_bound_without_H3K27ac,percent_svbf7_unbound_without_H3K27ac)
etat_svb = c("svbF7_bound","svb_unbound")
H3K27ac_absent = c(percent_svbf7_bound_without_H3K27ac,percent_svbf7_unbound_without_H3K27ac)
H3K27ac_present = c(percent_svbf7_H3K27ac_bound,percent_svbf7_H3K27ac_unbound)
data_H3K27ac_ctrl = data.frame(etat_svb,H3K27ac_absent,H3K27ac_present)
datatable(data_H3K27ac_ctrl,rownames = F,filter = "none",colnames = c("Regions without H3K27ac","Regions with H3K27ac" ))
fig1 = plot_ly(data_H3K27ac_ctrl, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig1 = fig1 %>% add_trace(y = ~H3K27ac_present, name = "H3K27ac absent", color = I("grey"))
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb ( Ctrl Condtion) ", barmode = "stack")
fig1
fig1 = plot_ly(data_H3K27ac_ctrl, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig1 = fig1 %>% add_trace(y = ~H3K27ac_present, name = "H3K27ac absent", color = I("grey"))
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb ( Ctrl Condtion) ")
fig1
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 unbound | 596 | 1191 |
| absent svbF7 unbound | 5081 | 8995 |
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 bound | 43 | 2 |
| absent svbF7 bound | 5638 | 10579 |
pvalue_fixe = phyper(43 - 1, 45, 16262 - 45, 5681)
pvalue_nonfixe = phyper(596 - 1, 1787, 15863 - 1787, 5677)
presence = c(43,5638)
absence = c(2,10579)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27ac_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27ac_fixe)
presence = c(596,5081)
absence = c(1191,8995)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27ac_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27ac_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 0.0103025
La pvalue du test de fisher pour les motifs fixé est de 8.909640810^{-18} Celle du test de fisher pour les motifs non fixé est de 0.0226837`
total_svbF7_unbound_H3K27ac = 596 + 1191
total_svbF7_bound_H3K27ac = 43 + 2
percent_svbf7_H3K27ac_unbound = round(100 * 596 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_unbound_without_H3K27ac = round(100 * 1191 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_H3K27ac_bound = round(100 * 43 / total_svbF7_bound_H3K27ac, 2 )
percent_svbf7_bound_without_H3K27ac = round(100 * 2 / total_svbF7_bound_H3K27ac, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K27ac_absent = c(percent_svbf7_bound_without_H3K27ac,percent_svbf7_unbound_without_H3K27ac)
H3K27ac_present = c(percent_svbf7_H3K27ac_bound,percent_svbf7_H3K27ac_unbound)
data_H3K27ac_act = data.frame(etat_svb,H3K27ac_absent,H3K27ac_present)
datatable(data_H3K27ac_act,rownames = F,filter = "none",colnames = c("Regions without H3K27ac","Regions with H3K27ac" ))
fig1 = plot_ly(data_H3K27ac_act, x = ~etat_svb,y = ~H3K27ac_absent, type = "bar",name = "H3K27ac absent", color = I("grey"))
fig1 = fig1 %>% add_trace(y = ~H3K27ac_present, name = "H3K27ac present", color = I("blue"))
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb ( Act Condtion) ", barmode = "stack")
fig1
fig1 = plot_ly(data_H3K27ac_act, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig1 = fig1 %>% add_trace(y = ~H3K27ac_absent, name = "H3K27ac absent", color = I("grey"))
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb ( Act Condtion) ", barmode = "stack")
fig1
fig1 = plot_ly(data_H3K27ac_act, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig1 = fig1 %>% add_trace(y = ~H3K27ac_absent, name = "H3K27ac absent", color = I("grey"))
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb ( Act Condtion) ")
fig1
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 unbound | 594 | 1193 |
| absent svbF7 unbound | 5037 | 8903 |
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 bound | 38 | 7 |
| absent svbF7 bound | 5596 | 10479 |
pvalue_fixe = phyper(38 - 1, 45, 16120 - 45, 5634)
pvalue_nonfixe = phyper(594 - 1, 1787, 15727 - 1787, 5631)
presence = c(38,5596)
absence = c(7,10479)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27ac_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27ac_fixe)
presence = c(594,5037)
absence = c(1193,8903)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27ac_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27ac_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 0.007383
La pvalue du test de fisher pour les motifs fixé est de 1.035723410^{-11} Celle du test de fisher pour les motifs non fixé est de 0.0170752`
total_svbF7_unbound_H3K27ac = 594 + 1193
total_svbF7_bound_H3K27ac = 38 + 7
percent_svbf7_H3K27ac_unbound = round(100 * 594 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_unbound_without_H3K27ac = round(100 * 1193 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_H3K27ac_bound = round(100 * 38 / total_svbF7_bound_H3K27ac, 2 )
percent_svbf7_bound_without_H3K27ac = round(100 * 7 / total_svbF7_bound_H3K27ac, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K27ac_absent = c(percent_svbf7_bound_without_H3K27ac,percent_svbf7_unbound_without_H3K27ac)
H3K27ac_present = c(percent_svbf7_H3K27ac_bound,percent_svbf7_H3K27ac_unbound)
data_H3K27ac_rep = data.frame(etat_svb,H3K27ac_absent,H3K27ac_present)
datatable(data_H3K27ac_rep,rownames = F,filter = "none",colnames = c("Regions without H3K27ac","Regions with H3K27ac" ))
fig1 = plot_ly(data_H3K27ac_rep, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig1 = fig1 %>% add_trace(y = ~H3K27ac_absent, name = "H3K27ac absent", color = I("grey"))
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb ( Rep condition) ", barmode = "stack")
fig1
fig1 = plot_ly(data_H3K27ac_rep, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig1 = fig1 %>% add_trace(y = ~H3K27ac_absent, name = "H3K27ac absent", color = I("grey"))
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb ( Rep condition) ")
fig1
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 unbound | 2268 | 0 |
| absent svbF7 unbound | 12859 | 0 |
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 bound | 43 | 2 |
| absent svbF7 bound | 15084 | 220 |
pvalue_fixe = phyper(43 - 1, 45, 15349 - 45, 15127)
pvalue_nonfixe = phyper(2268 - 1, 1787, 15127 - 1787, 15127)
presence = c(43,15084)
absence = c(2,220)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27me3_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27me3_fixe)
presence = c(2268,15084)
absence = c(0,0)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27me3_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27me3_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 0.0271347 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 0.1378574 Celle du test de fisher pour les motifs non fixé est de 1`
total_svbF7_unbound_H3K27me3 = 2268 + 0
total_svbF7_bound_H3K27me3 = 43 + 2
percent_svbf7_H3K27me3_unbound = round(100 * 2268 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_unbound_without_H3K27me3 = round(100 * 0 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_H3K27me3_bound = round(100 * 43 / total_svbF7_bound_H3K27me3, 2 )
percent_svbf7_bound_without_H3K27me3 = round(100 * 2 / total_svbF7_bound_H3K27me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K27me3_absent = c(percent_svbf7_bound_without_H3K27me3,percent_svbf7_unbound_without_H3K27me3)
H3K27me3_present = c(percent_svbf7_H3K27me3_bound,percent_svbf7_H3K27me3_unbound)
data_H3K27me3_ctrl = data.frame(etat_svb,H3K27me3_absent,H3K27me3_present)
datatable(data_H3K27me3_ctrl,rownames = F,filter = "none",colnames = c("Regions without H3K27me3","Regions with H3K27me3" ))
fig2 = plot_ly(data_H3K27me3_ctrl, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color =I("purple"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_absent, name = "H3K27me3 absent",color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb (Ctrl condition)", barmode = "stack")
fig2
fig2 = plot_ly(data_H3K27me3_ctrl, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color =I("purple"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_absent, name = "H3K27me3 absent",color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb (Ctrl condition)")
fig2
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 unbound | 2180 | 0 |
| absent svbF7 unbound | 12129 | 19 |
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 bound | 46 | 0 |
| absent svbF7 bound | 14263 | 344 |
pvalue_fixe = phyper(46 - 1, 45, 14653 - 45, 14309)
pvalue_nonfixe = phyper(2180 - 1, 1787, 14328 - 1787, 14328)
presence = c(46,14263)
absence = c(0,19)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27me3_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27me3_fixe)
presence = c(2180,12129)
absence = c(0,19)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27me3_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27me3_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 1 Celle du test de fisher pour les motifs non fixé est de 0.1002134`
total_svbF7_unbound_H3K27me3 = 2180+ 0
total_svbF7_bound_H3K27me3 = 46 + 0
percent_svbf7_H3K27me3_unbound = round(100 * 2180 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_unbound_without_H3K27me3 = round(100 * 0 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_H3K27me3_bound = round(100 * 46 / total_svbF7_bound_H3K27me3, 2 )
percent_svbf7_bound_without_H3K27me3 = round(100 * 0 / total_svbF7_bound_H3K27me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K27me3_absent = c(percent_svbf7_bound_without_H3K27me3,percent_svbf7_unbound_without_H3K27me3)
H3K27me3_present = c(percent_svbf7_H3K27me3_bound,percent_svbf7_H3K27me3_unbound)
data_H3K27me3_act = data.frame(etat_svb,H3K27me3_absent,H3K27me3_present)
datatable(data_H3K27me3_act,rownames = F,filter = "none",colnames = c("Regions without H3K27me3","Regions with H3K27me3" ))
fig2 = plot_ly(data_H3K27me3_act, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color =I("purple"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_absent, name = "H3K27me3 absent",color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb ( Act condition ) ", barmode = "stack")
fig2
fig2 = plot_ly(data_H3K27me3_act, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color =I("purple"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_absent, name = "H3K27me3 absent",color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb ( Act condition ) ")
fig2
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 unbound | 223 | 0 |
| absent svbF7 unbound | 13048 | 0 |
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 bound | 48 | 0 |
| absent svbF7 bound | 15253 | 0 |
pvalue_fixe = phyper(48 - 1, 45, 15301 - 45, 15301)
pvalue_nonfixe = phyper(2253 - 1, 1787, 15301 - 1787, 15301)
presence = c(48,15253)
absence = c(0,0)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27me3_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27me3_fixe)
presence = c(223,13048)
absence = c(0,0)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27me3_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27me3_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 1 Celle du test de fisher pour les motifs non fixé est de 1`
total_svbF7_unbound_H3K27me3 = 223+ 0
total_svbF7_bound_H3K27me3 = 48 + 0
percent_svbf7_H3K27me3_unbound = round(100 * 223 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_unbound_without_H3K27me3 = round(100 * 0 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_H3K27me3_bound = round(100 * 48 / total_svbF7_bound_H3K27me3, 2 )
percent_svbf7_bound_without_H3K27me3 = round(100 * 0 / total_svbF7_bound_H3K27me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K27me3_absent = c(percent_svbf7_bound_without_H3K27me3,percent_svbf7_unbound_without_H3K27me3)
H3K27me3_present = c(percent_svbf7_H3K27me3_bound,percent_svbf7_H3K27me3_unbound)
data_H3K27me3_rep = data.frame(etat_svb,H3K27me3_absent,H3K27me3_present)
datatable(data_H3K27me3_rep,rownames = F,filter = "none",colnames = c("Regions without H3K27me3","Regions with H3K27me3" ))
fig2 = plot_ly(data_H3K27me3_rep, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color =I("purple"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_absent, name = "H3K27me3 absent",color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb ( Rep condition ) ", barmode = "stack")
fig2
fig2 = plot_ly(data_H3K27me3_rep, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color =I("purple"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_absent, name = "H3K27me3 absent",color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb ( Rep condition ) ")
fig2
Je regarde ici l’enrichisement en histones des motifs de Svb en présence des différentes formes de Svb ( Act/ Rep) et Ctrl
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 unbound | 1434 | 366 |
| absent svbF7 unbound | 8757 | 4425 |
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 bound | 48 | 0 |
| absent svbF7 bound | 10148 | 4328 |
pvalue_fixe = phyper(48 - 1, 30, 14524 - 30, 10196)
pvalue_nonfixe = phyper(1434 - 1, 1800, 14982 - 1800, 10191)
presence = c(48,10148)
absence = c(0,4328)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me1_fixe_ctrl = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me1_fixe_ctrl)
presence = c(1434,8757)
absence = c(366,4425)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me1_nonfixe_ctrl = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me1_nonfixe_ctrl)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 6.868377910^{-8} Celle du test de fisher pour les motifs non fixé est de 1.65729710^{-31}`
total_svbF7_unbound = 1434 + 366
total_svbF7_bound = 48 + 0
percent_svbf7_H3K4me1_unbound = round(100 * 1434 / total_svbF7_unbound, 2 )
percent_svbf7_unbound_without_H3K4me1 = round(100 * 366 / total_svbF7_unbound, 2 )
percent_svbf7_H3K4me1_bound = round(100 * 48 / total_svbF7_bound, 2 )
percent_svbf7_bound_without_H3K4me1 = round(100 * 0 / total_svbF7_bound, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me1_absent = c(percent_svbf7_bound_without_H3K4me1,percent_svbf7_unbound_without_H3K4me1)
H3K4me1_present = c(percent_svbf7_H3K4me1_bound,percent_svbf7_H3K4me1_unbound)
data_H3K4me1_ctrl = data.frame(etat_svb,H3K4me1_absent,H3K4me1_present)
datatable(data_H3K4me1_ctrl,rownames = F,filter = "none", colnames = c("Regions without H3K4me1","Regions with H3K4me1" ))
fig3 = plot_ly(data_H3K4me1_ctrl, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig3 = fig3 %>% add_trace(y = ~H3K4me1_present, name = "H3K4me1 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb (Ctrl condition)", barmode = "stack")
fig3
fig3 = plot_ly(data_H3K4me1_ctrl, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig3 = fig3 %>% add_trace(y = ~H3K4me1_present, name = "H3K4me1 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb (Ctrl condition)")
fig3
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 unbound | 1657 | 143 |
| absent svbF7 unbound | 10587 | 3398 |
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 bound | 47 | 0 |
| absent svbF7 bound | 12203 | 3028 |
pvalue_fixe = phyper(47 - 1, 30, 15278 - 30, 12250)
pvalue_nonfixe = phyper(1657 - 1, 1800, 15785 - 1800, 12244)
presence = c(1657,10587)
absence = c(143,3398)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me1_fixe_act = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me1_fixe_act)
presence = c(47,0)
absence = c(12203,3028)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me1_nonfixe_act = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me1_nonfixe_act)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 1.853204510^{-66} Celle du test de fisher pour les motifs non fixé est de 5.716693710^{-5}`
total_svbF7_unbound = 1657 + 143
total_svbF7_bound = 47 + 0
percent_svbf7_H3K4me1_unbound = round(100 * 1657 / total_svbF7_unbound, 2 )
percent_svbf7_unbound_without_H3K4me1 = round(100 * 143 / total_svbF7_unbound, 2 )
percent_svbf7_H3K4me1_bound = round(100 * 47 / total_svbF7_bound, 2 )
percent_svbf7_bound_without_H3K4me1 = round(100 * 0 / total_svbF7_bound, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me1_absent = c(percent_svbf7_bound_without_H3K4me1,percent_svbf7_unbound_without_H3K4me1)
H3K4me1_present = c(percent_svbf7_H3K4me1_bound,percent_svbf7_H3K4me1_unbound)
data_H3K4me1_act = data.frame(etat_svb,H3K4me1_absent,H3K4me1_present)
datatable(data_H3K4me1_act,rownames = F,filter = "none", colnames = c("Regions without H3K4me1","Regions with H3K4me1" ))
fig3 = plot_ly(data_H3K4me1_act, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig3 = fig3 %>% add_trace(y = ~H3K4me1_absent, name = "H3K4me1 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb (Act condition)", barmode = "stack")
fig3
fig3 = plot_ly(data_H3K4me1_act, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig3 = fig3 %>% add_trace(y = ~H3K4me1_absent, name = "H3K4me1 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb (Act condition)")
fig3
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 unbound | 1580 | 220 |
| absent svbF7 unbound | 10217 | 3582 |
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 bound | 46 | 0 |
| absent svbF7 bound | 11756 | 3301 |
pvalue_fixe = phyper(46 - 1, 30, 15103 - 30, 11802)
pvalue_nonfixe = phyper(1508 - 1, 1800, 15599 - 1800, 11797)
presence = c(46,11756)
absence = c(0,3301)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me1_fixe_rep = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me1_fixe_rep)
presence = c(1580,10217)
absence = c(220,3582)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me1_nonfixe_rep = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me1_nonfixe_rep)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 1.783063810^{-5} Celle du test de fisher pour les motifs non fixé est de 4.847625110^{-42}`
total_svbF7_unbound = 1580 + 220
total_svbF7_bound = 46 + 0
percent_svbf7_H3K4me1_unbound = round(100 * 1580 / total_svbF7_unbound, 2 )
percent_svbf7_unbound_without_H3K4me1 = round(100 * 220 / total_svbF7_unbound, 2 )
percent_svbf7_H3K4me1_bound = round(100 * 46 / total_svbF7_bound, 2 )
percent_svbf7_bound_without_H3K4me1 = round(100 * 0 / total_svbF7_bound, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me1_absent = c(percent_svbf7_bound_without_H3K4me1,percent_svbf7_unbound_without_H3K4me1)
H3K4me1_present = c(percent_svbf7_H3K4me1_bound,percent_svbf7_H3K4me1_unbound)
data_H3K4me1_rep = data.frame(etat_svb,H3K4me1_absent,H3K4me1_present)
datatable(data_H3K4me1_rep,rownames = F,filter = "none", colnames = c("Regions without H3K4me1","Regions with H3K4me1" ))
fig3 = plot_ly(data_H3K4me1_rep, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig3 = fig3 %>% add_trace(y = ~H3K4me1_absent, name = "H3K4me1 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb (Rep condition)", barmode = "stack")
fig3
fig3 = plot_ly(data_H3K4me1_rep, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig3 = fig3 %>% add_trace(y = ~H3K4me1_absent, name = "H3K4me1 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb (Rep condition)")
fig3
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 unbound | 1087 | 713 |
| absent svbF7 unbound | 9558 | 6543 |
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 bound | 31 | 0 |
| absent svbF7 bound | 10614 | 6606 |
pvalue_fixe = phyper(31 - 1, 30, 17251 - 30, 10645)
pvalue_nonfixe = phyper(1087 - 1, 1800, 17901 - 1800, 10645)
presence = c(31,10614)
absence = c(0,6606)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me3_fixe_ctrl = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me3_fixe_ctrl)
presence = c(1087,9558)
absence = c(713,6543)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me3_nonfixe_ctrl = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me3_nonfixe_ctrl)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 0.7925253
La pvalue du test de fisher pour les motifs fixé est de 5.534338610^{-7} Celle du test de fisher pour les motifs non fixé est de 0.4037`
total_svbF7_unbound_H3K4me3 = 1087 + 713
total_svbF7_bound_H3K4me3 = 31 + 0
percent_svbf7_H3K4me3_unbound = round(100 * 1087 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_unbound_without_H3K4me3 = round(100 * 713 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_H3K4me3_bound = round(100 * 31 / total_svbF7_bound_H3K4me3, 2 )
percent_svbf7_bound_without_H3K4me3 = round(100 * 0 / total_svbF7_bound_H3K4me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me3_absent = c(percent_svbf7_bound_without_H3K4me3,percent_svbf7_unbound_without_H3K4me3)
H3K4me3_present = c(percent_svbf7_H3K4me3_bound,percent_svbf7_H3K4me3_unbound)
data_H3K4me3_ctrl = data.frame(etat_svb,H3K4me3_absent,H3K4me3_present)
datatable(data_H3K4me3_ctrl,rownames = F,filter = "none",colnames = c("Regions without H3K4me3","Regions with H3K4me3" ))
fig4 = plot_ly(data_H3K4me3_ctrl, x = ~etat_svb,y = ~H3K4me3_present, type = "bar",name = "H3K4me3 present", color = I("pink"))
fig4 = fig4 %>% add_trace(y = ~H3K4me3_absent, name = "H3K4me3 absent", color = I("grey"))
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb (Ctrl condition)", barmode = "stack")
fig4
fig4 = plot_ly(data_H3K4me3_ctrl, x = ~etat_svb,y = ~H3K4me3_present, type = "bar",name = "H3K4me3 present", color = I("pink"))
fig4 = fig4 %>% add_trace(y = ~H3K4me3_absent, name = "H3K4me3 absent", color = I("grey"))
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb (Ctrl condition)")
fig4
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 unbound | 646 | 1154 |
| absent svbF7 unbound | 6593 | 9601 |
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 bound | 28 | 2 |
| absent svbF7 bound | 7212 | 10096 |
pvalue_fixe = phyper(28 - 1, 30, 17338 - 30, 7240)
pvalue_nonfixe = phyper(646 - 1, 1800, 17994 - 1800, 7239)
presence = c(28,7212)
absence = c(2,10096)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me3_fixe_act = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me3_fixe_act)
presence = c(646,6593)
absence = c(2,10096)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me3_nonfixe_act = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me3_nonfixe_act)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 3.076336810^{-5}
La pvalue du test de fisher pour les motifs fixé est de 3.624050310^{-9} Celle du test de fisher pour les motifs non fixé est de 1.811466310^{-248}`
total_svbF7_unbound_H3K4me3 = 646 + 1154
total_svbF7_bound_H3K4me3 = 28 + 2
percent_svbf7_H3K4me3_unbound = round(100 * 646 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_unbound_without_H3K4me3 = round(100 * 1154 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_H3K4me3_bound = round(100 * 28 / total_svbF7_bound_H3K4me3, 2 )
percent_svbf7_bound_without_H3K4me3 = round(100 * 2/ total_svbF7_bound_H3K4me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me3_absent = c(percent_svbf7_bound_without_H3K4me3,percent_svbf7_unbound_without_H3K4me3)
H3K4me3_present = c(percent_svbf7_H3K4me3_bound,percent_svbf7_H3K4me3_unbound)
data_H3K4me3_act = data.frame(etat_svb,H3K4me3_absent,H3K4me3_present)
datatable(data_H3K4me3_act,rownames = F,filter = "none",colnames = c("Regions without H3K4me3","Regions with H3K4me3" ))
fig4 = plot_ly(data_H3K4me3_act, x = ~etat_svb,y = ~H3K4me3_present, type = "bar",name = "H3K4me3 present", color = I("pink"))
fig4 = fig4 %>% add_trace(y = ~H3K4me3_absent, name = "H3K4me3 absent", color = I("grey"))
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb (Act condition)", barmode = "stack")
fig4
fig4 = plot_ly(data_H3K4me3_act, x = ~etat_svb,y = ~H3K4me3_present, type = "bar",name = "H3K4me3 present", color = I("pink"))
fig4 = fig4 %>% add_trace(y = ~H3K4me3_absent, name = "H3K4me3 absent", color = I("grey"))
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb (Act condition)")
fig4
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 unbound | 444 | 1356 |
| absent svbF7 unbound | 4350 | 10691 |
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 bound | 28 | 2 |
| absent svbF7 bound | 4764 | 11467 |
pvalue_fixe = phyper(28 - 1, 30, 16264 - 30, 4795)
pvalue_nonfixe = phyper(444 - 1, 1800, 16841 - 1800, 4794)
presence = c(444,4350)
absence = c(1356,10691)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me3_fixe_rep = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me3_fixe_rep)
presence = c(28,2)
absence = c(4764,11467)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me3_nonfixe_rep = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me3_nonfixe_rep)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 5.822629410^{-5}
La pvalue du test de fisher pour les motifs fixé est de 1.362101910^{-4} Celle du test de fisher pour les motifs non fixé est de 2.932863510^{-13}`
total_svbF7_unbound_H3K4me3 = 444 + 1356
total_svbF7_bound_H3K4me3 = 28 + 2
percent_svbf7_H3K4me3_unbound = round(100 * 444 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_unbound_without_H3K4me3 = round(100 * 1356 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_H3K4me3_bound = round(100 * 28 / total_svbF7_bound_H3K4me3, 2 )
percent_svbf7_bound_without_H3K4me3 = round(100 * 2 / total_svbF7_bound_H3K4me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me3_absent = c(percent_svbf7_bound_without_H3K4me3,percent_svbf7_unbound_without_H3K4me3)
H3K4me3_present = c(percent_svbf7_H3K4me3_bound,percent_svbf7_H3K4me3_unbound)
data_H3K4me3_rep = data.frame(etat_svb,H3K4me3_absent,H3K4me3_present)
datatable(data_H3K4me3_rep,rownames = F,filter = "none",colnames = c("Regions without H3K4me3","Regions with H3K4me3" ))
fig4 = plot_ly(data_H3K4me3_rep, x = ~etat_svb,y = ~H3K4me3_present, type = "bar",name = "H3K4me3 present", color = I("pink"))
fig4 = fig4 %>% add_trace(y = ~H3K4me3_absent, name = "H3K4me3 absent", color = I("grey"))
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb (Rep condition)", barmode = "stack")
fig4
fig4 = plot_ly(data_H3K4me3_rep, x = ~etat_svb,y = ~H3K4me3_present, type = "bar",name = "H3K4me3 present", color = I("pink"))
fig4 = fig4 %>% add_trace(y = ~H3K4me3_absent, name = "H3K4me3 absent", color = I("grey"))
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb (Rep condition)")
fig4
total_K4me1_S2 = 8782
total_K4me3_S2 = 4812
rapp_fixe = round((contingence_H3K4me1_fixe_ctrl[1,1] / total_K4me1_S2 ) / (contingence_H3K4me3_fixe_ctrl[1,1] / total_K4me3_S2),2)
rapp_nonfixe = round((contingence_H3K4me1_nonfixe_ctrl[1,1] / total_K4me1_S2) / (contingence_H3K4me3_nonfixe_ctrl[1,1] / total_K4me3_S2) ,2)
Il y a 0.85 fois de H3K4me1 que de H3K4me3 fixé.
Il y a 0.72 fois de H3K4me1 que de H3K4me3 non fixé.
total_K4me1_S2 = 8782
total_K4me3_S2 = 4812
rapp_fixe = round((contingence_H3K4me1_fixe_act [1,1] / total_K4me1_S2 ) / (contingence_H3K4me3_fixe_act[1,1] / total_K4me3_S2),2)
rapp_nonfixe = round((contingence_H3K4me1_nonfixe_act[1,1] / total_K4me1_S2) / (contingence_H3K4me3_nonfixe_act[1,1] / total_K4me3_S2) ,2)
Il y a 32.43 fois de H3K4me1 que de H3K4me3 fixé.
Il y a 0.04 fois de H3K4me1 que de H3K4me3 non fixé.
total_K4me1_S2 = 8782
total_K4me3_S2 = 4812
rapp_fixe = round((contingence_H3K4me1_fixe_rep[1,1] / total_K4me1_S2 ) / (contingence_H3K4me3_fixe_rep[1,1] / total_K4me3_S2),2)
rapp_nonfixe = round((contingence_H3K4me1_nonfixe_rep[1,1] / total_K4me1_S2) / (contingence_H3K4me3_nonfixe_rep[1,1] / total_K4me3_S2) ,2)
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 unbound | 612 | 1188 |
| absent svbF7 unbound | 5020 | 8887 |
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 bound | 34 | 0 |
| absent svbF7 bound | 5601 | 9570 |
pvalue_fixe = phyper(34 - 1, 30, 15205 - 30, 5635)
pvalue_nonfixe = phyper(612 - 1, 1800, 15707 - 1800, 5632)
presence = c(34,5601)
absence = c(0,9570)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27ac_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27ac_fixe)
presence = c(612,5020)
absence = c(1188,8887)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27ac_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27ac_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 0.0378741
La pvalue du test de fisher pour les motifs fixé est de 2.068081110^{-15} Celle du test de fisher pour les motifs non fixé est de 0.0847469`
total_svbF7_unbound_H3K27ac = 612 + 1188
total_svbF7_bound_H3K27ac = 34 + 0
percent_svbf7_H3K27ac_unbound = round(100 * 612 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_unbound_without_H3K27ac = round(100 * 1188 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_H3K27ac_bound = round(100 * 34 / total_svbF7_bound_H3K27ac, 2 )
percent_svbf7_bound_without_H3K27ac = round(100 * 0 / total_svbF7_bound_H3K27ac, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K27ac_absent = c(percent_svbf7_bound_without_H3K27ac,percent_svbf7_unbound_without_H3K27ac)
H3K27ac_present = c(percent_svbf7_H3K27ac_bound,percent_svbf7_H3K27ac_unbound)
data_H3K27ac_ctrl = data.frame(etat_svb,H3K27ac_absent,H3K27ac_present)
datatable(data_H3K27ac_ctrl,rownames = F,filter = "none",colnames = c("Regions without H3K27ac","Regions with H3K27ac" ))
fig1 = plot_ly(data_H3K27ac_ctrl, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig1 = fig1 %>% add_trace(y = ~H3K27ac_absent, name = "H3K27ac absent", color = I("grey"))
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb ( Ctrl condition)", barmode = "stack")
fig1
fig1 = plot_ly(data_H3K27ac_ctrl, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig1 = fig1 %>% add_trace(y = ~H3K27ac_absent, name = "H3K27ac absent", color = I("grey"))
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb ( Ctrl condition)")
fig1
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 unbound | 606 | 1194 |
| absent svbF7 unbound | 5072 | 8991 |
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 bound | 35 | 0 |
| absent svbF7 bound | 5646 | 9670 |
pvalue_fixe = phyper(35 - 1, 30, 15351 - 30, 5681)
pvalue_nonfixe = phyper(606 - 1, 1800, 15863 - 1800, 5678)
presence = c(35,5646)
absence = c(0,9670)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27ac_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27ac_fixe)
presence = c(606,5072)
absence = c(1194,8991)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27ac_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27ac_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 0.021082
La pvalue du test de fisher pour les motifs fixé est de 7.26694110^{-16} Celle du test de fisher pour les motifs non fixé est de 0.0472022`
total_svbF7_unbound_H3K27ac = 606 + 1194
total_svbF7_bound_H3K27ac = 35 + 0
percent_svbf7_H3K27ac_unbound = round(100 * 606 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_unbound_without_H3K27ac = round(100 * 1194 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_H3K27ac_bound = round(100 * 35 / total_svbF7_bound_H3K27ac, 2 )
percent_svbf7_bound_without_H3K27ac = round(100 * 0 / total_svbF7_bound_H3K27ac, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K27ac_absent = c(percent_svbf7_bound_without_H3K27ac,percent_svbf7_unbound_without_H3K27ac)
H3K27ac_present = c(percent_svbf7_H3K27ac_bound,percent_svbf7_H3K27ac_unbound)
data_H3K27ac_act = data.frame(etat_svb,H3K27ac_absent,H3K27ac_present)
datatable(data_H3K27ac_act,rownames = F,filter = "none",colnames = c("Regions without H3K27ac","Regions with H3K27ac" ))
fig1 = plot_ly(data_H3K27ac_act, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig1 = fig1 %>% add_trace(y = ~H3K27ac_absent, name = "H3K27ac absent", color = I("grey"))
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb ( Act Condtion) ", barmode = "stack")
fig1
fig1 = plot_ly(data_H3K27ac_act, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig1 = fig1 %>% add_trace(y = ~H3K27ac_absent, name = "H3K27ac absent", color = I("grey"))
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb ( Act Condtion) ")
fig1
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 unbound | 602 | 1198 |
| absent svbF7 unbound | 5030 | 8898 |
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 bound | 31 | 0 |
| absent svbF7 bound | 5603 | 9590 |
pvalue_fixe = phyper(31 - 1, 30, 15224 - 30, 5634)
pvalue_nonfixe = phyper(602 - 1, 1800, 15728 - 1800, 5632)
presence = c(31,5603)
absence = c(0,9590)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27ac_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27ac_fixe)
presence = c(602,5030)
absence = c(1198,8898)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27ac_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27ac_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 0.0119846
La pvalue du test de fisher pour les motifs fixé est de 3.929115610^{-14} Celle du test de fisher pour les motifs non fixé est de 0.0264009`
total_svbF7_unbound_H3K27ac = 602 + 1198
total_svbF7_bound_H3K27ac = 31 + 0
percent_svbf7_H3K27ac_unbound = round(100 * 602 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_unbound_without_H3K27ac = round(100 * 1198 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_H3K27ac_bound = round(100 * 31 / total_svbF7_bound_H3K27ac, 2 )
percent_svbf7_bound_without_H3K27ac = round(100 * 0 / total_svbF7_bound_H3K27ac, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K27ac_absent = c(percent_svbf7_bound_without_H3K27ac,percent_svbf7_unbound_without_H3K27ac)
H3K27ac_present = c(percent_svbf7_H3K27ac_bound,percent_svbf7_H3K27ac_unbound)
data_H3K27ac_rep = data.frame(etat_svb,H3K27ac_absent,H3K27ac_present)
datatable(data_H3K27ac_rep,rownames = F,filter = "none",colnames = c("Regions without H3K27ac","Regions with H3K27ac" ))
fig1 = plot_ly(data_H3K27ac_rep, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig1 = fig1 %>% add_trace(y = ~H3K27ac_absent, name = "H3K27ac absent", color = I("grey"))
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb ( Rep condition) ", barmode = "stack")
fig1
fig1 = plot_ly(data_H3K27ac_rep, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig1 = fig1 %>% add_trace(y = ~H3K27ac_absent, name = "H3K27ac absent", color = I("grey"))
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb ( Rep condition) ")
fig1
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 unbound | 2278 | 0 |
| absent svbF7 unbound | 12849 | 0 |
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 bound | 33 | 0 |
| absent svbF7 bound | 15094 | 0 |
pvalue_fixe = phyper(33 - 1, 30, 15127 - 30, 15127)
pvalue_nonfixe = phyper(2278 - 1, 1800, 15127 - 1800, 15127)
presence = c(33,15094)
absence = c(0,0)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27me3_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27me3_fixe)
presence = c(2278,15094)
absence = c(0,0)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27me3_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27me3_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 1 Celle du test de fisher pour les motifs non fixé est de 1`
total_svbF7_unbound_H3K27me3 = 2278 + 0
total_svbF7_bound_H3K27me3 = 33 + 0
percent_svbf7_H3K27me3_unbound = round(100 * 2278 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_unbound_without_H3K27me3 = round(100 * 0 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_H3K27me3_bound = round(100 * 33 / total_svbF7_bound_H3K27me3, 2 )
percent_svbf7_bound_without_H3K27me3 = round(100 * 0 / total_svbF7_bound_H3K27me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K27me3_absent = c(percent_svbf7_bound_without_H3K27me3,percent_svbf7_unbound_without_H3K27me3)
H3K27me3_present = c(percent_svbf7_H3K27me3_bound,percent_svbf7_H3K27me3_unbound)
data_H3K27me3_ctrl = data.frame(etat_svb,H3K27me3_absent,H3K27me3_present)
datatable(data_H3K27me3_ctrl,rownames = F,filter = "none",colnames = c("Regions without H3K27me3","Regions with H3K27me3" ))
fig2 = plot_ly(data_H3K27me3_ctrl, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color =I("purple"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_absent, name = "H3K27me3 absent",color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb (Ctrl condition)", barmode = "stack")
fig2
fig2 = plot_ly(data_H3K27me3_ctrl, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color =I("purple"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_absent, name = "H3K27me3 absent",color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb (Ctrl condition)")
fig2
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 unbound | 2192 | 0 |
| absent svbF7 unbound | 12117 | 0 |
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 bound | 35 | 0 |
| absent svbF7 bound | 14274 | 0 |
pvalue_fixe = phyper(35 - 1, 30, 14309 - 30, 14309)
pvalue_nonfixe = phyper(2192 - 1, 1800, 14329 - 1800, 14309)
presence = c(35,14274)
absence = c(0,0)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27me3_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27me3_fixe)
presence = c(2192,14274)
absence = c(0,0)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27me3_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27me3_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 1 Celle du test de fisher pour les motifs non fixé est de 1`
total_svbF7_unbound_H3K27me3 = 2192+ 0
total_svbF7_bound_H3K27me3 = 35 + 0
percent_svbf7_H3K27me3_unbound = round(100 * 2192 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_unbound_without_H3K27me3 = round(100 * 0 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_H3K27me3_bound = round(100 * 35 / total_svbF7_bound_H3K27me3, 2 )
percent_svbf7_bound_without_H3K27me3 = round(100 * 0 / total_svbF7_bound_H3K27me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K27me3_absent = c(percent_svbf7_bound_without_H3K27me3,percent_svbf7_unbound_without_H3K27me3)
H3K27me3_present = c(percent_svbf7_H3K27me3_bound,percent_svbf7_H3K27me3_unbound)
data_H3K27me3_act = data.frame(etat_svb,H3K27me3_absent,H3K27me3_present)
datatable(data_H3K27me3_act,rownames = F,filter = "none",colnames = c("Regions without H3K27me3","Regions with H3K27me3" ))
fig2 = plot_ly(data_H3K27me3_act, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color =I("purple"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_absent, name = "H3K27me3 absent",color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb ( Act condition ) ", barmode = "stack")
fig2
fig2 = plot_ly(data_H3K27me3_act, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color =I("purple"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_absent, name = "H3K27me3 absent",color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb ( Act condition ) ")
fig2
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 unbound | 2265 | 0 |
| absent svbF7 unbound | 13036 | 0 |
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 bound | 35 | 0 |
| absent svbF7 bound | 15266 | 0 |
pvalue_fixe = phyper(35 - 1, 30, 15301 - 30, 15301)
pvalue_nonfixe = phyper(2265 - 1, 1800, 15301 - 1800, 15301)
presence = c(35,15266)
absence = c(0,0)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27me3_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27me3_fixe)
presence = c(2265,13036)
absence = c(0,0)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27me3_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27me3_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 1 Celle du test de fisher pour les motifs non fixé est de 1`
total_svbF7_unbound_H3K27me3 = 2265+ 0
total_svbF7_bound_H3K27me3 = 35 + 0
percent_svbf7_H3K27me3_unbound = round(100 * 2265 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_unbound_without_H3K27me3 = round(100 * 0 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_H3K27me3_bound = round(100 * 35 / total_svbF7_bound_H3K27me3, 2 )
percent_svbf7_bound_without_H3K27me3 = round(100 * 0 / total_svbF7_bound_H3K27me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K27me3_absent = c(percent_svbf7_bound_without_H3K27me3,percent_svbf7_unbound_without_H3K27me3)
H3K27me3_present = c(percent_svbf7_H3K27me3_bound,percent_svbf7_H3K27me3_unbound)
data_H3K27me3_rep = data.frame(etat_svb,H3K27me3_absent,H3K27me3_present)
datatable(data_H3K27me3_rep,rownames = F,filter = "none",colnames = c("Regions without H3K27me3","Regions with H3K27me3" ))
fig2 = plot_ly(data_H3K27me3_rep, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color =I("purple"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_absent, name = "H3K27me3 absent",color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb ( Rep condition ) ", barmode = "stack")
fig2
fig2 = plot_ly(data_H3K27me3_rep, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color =I("purple"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_absent, name = "H3K27me3 absent",color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb ( Rep condition ) ")
fig2
data = merge(data_H3K4me1_ctrl,data_H3K4me1_act, by = "etat_svb" )
data = merge(data,data_H3K4me1_rep,by = "etat_svb")
data = merge(data,data_H3K4me3_ctrl, by = "etat_svb")
data = merge(data, data_H3K4me3_act, by = "etat_svb")
data = merge(data, data_H3K4me3_rep, by = "etat_svb")
data = merge(data, data_H3K27ac_ctrl, by = "etat_svb")
data = merge(data, data_H3K27ac_act, by = "etat_svb")
data = merge(data, data_H3K27ac_rep, by = "etat_svb")
data = merge(data, data_H3K27me3_ctrl, by = "etat_svb")
data = merge(data, data_H3K27me3_act, by = "etat_svb")
data = merge(data, data_H3K27me3_rep, by = "etat_svb")
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 unbound | 695 | 428 |
| absent svbF7 unbound | 6067 | 12192 |
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 bound | 504 | 285 |
| absent svbF7 bound | 6258 | 11859 |
pvalue_fixe = phyper(504 - 1, 789, 18906 - 789, 6762)
pvalue_nonfixe = phyper(695 - 1, 1123, 19382 - 1123, 6762)
presence = c(504,6258)
absence = c(285,11859)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27me3_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27me3_fixe)
presence = c(695,6067)
absence = c(428,12192)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27me3_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27me3_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 3.027742410^{-60} Celle du test de fisher pour les motifs non fixé est de 3.396497310^{-80}`
total_svbF7_unbound_H3K27me3 = 695 + 428
total_svbF7_bound_H3K27me3 = 504 + 285
percent_svbf7_H3K27me3_unbound = round(100 * 695 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_unbound_without_H3K27me3 = round(100 * 428 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_H3K27me3_bound = round(100 * 504 / total_svbF7_bound_H3K27me3, 2 )
percent_svbf7_bound_without_H3K27me3 = round(100 * 285 / total_svbF7_bound_H3K27me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K27me3_absent = c(percent_svbf7_bound_without_H3K27me3,percent_svbf7_unbound_without_H3K27me3)
H3K27me3_present = c(percent_svbf7_H3K27me3_bound,percent_svbf7_H3K27me3_unbound)
data_H3K27me3 = data.frame(etat_svb,H3K27me3_absent,H3K27me3_present)
datatable(data_H3K27me3,rownames = F,filter = "none",colnames = c("Regions without H3K27me3","Regions with H3K27me3" ))
fig2 = plot_ly(data_H3K27me3, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color = I("orange"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_absent, name = "H3K27me3 absent", color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 ( embryo 8-12h) enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig2
fig2 = plot_ly(data_H3K27me3, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color = I("orange"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_absent, name = "H3K27me3 absent", color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 ( embryo 8-12h) enrichment on svbF7 bound or not by Svb")
fig2
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 unbound | 689 | 434 |
| absent svbF7 unbound | 5917 | 12139 |
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 bound | 487 | 302 |
| absent svbF7 bound | 6119 | 11804 |
pvalue_fixe = phyper(487 - 1, 789, 18712 - 789, 6606)
pvalue_nonfixe = phyper(689 - 1, 1123, 19179 - 1123, 6606)
presence = c(487,6119)
absence = c(302,11804)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27me3_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27me3_fixe)
presence = c(689,5917)
absence = c(434,12139)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27me3_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27me3_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 1.816562810^{-53} Celle du test de fisher pour les motifs non fixé est de 4.020798110^{-80}`
total_svbF7_unbound_H3K27me3 = 689 + 434
total_svbF7_bound_H3K27me3 = 487 + 302
percent_svbf7_H3K27me3_unbound = round(100 * 689 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_unbound_without_H3K27me3 = round(100 * 434 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_H3K27me3_bound = round(100 * 487 / total_svbF7_bound_H3K27me3, 2 )
percent_svbf7_bound_without_H3K27me3 = round(100 * 302 / total_svbF7_bound_H3K27me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K27me3_absent = c(percent_svbf7_bound_without_H3K27me3,percent_svbf7_unbound_without_H3K27me3)
H3K27me3_present = c(percent_svbf7_H3K27me3_bound,percent_svbf7_H3K27me3_unbound)
data_H3K27me3 = data.frame(etat_svb,H3K27me3_absent,H3K27me3_present)
datatable(data_H3K27me3,rownames = F,filter = "none",colnames = c("Regions without H3K27me3","Regions with H3K27me3" ))
fig2 = plot_ly(data_H3K27me3, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color = I("purple"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_absent, name = "H3K27me3 absent", color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig2
fig2 = plot_ly(data_H3K27me3, x = ~etat_svb,y = ~H3K27me3_present, type = "bar",name = "H3K27me3 present", color = I("purple"))
fig2 = fig2 %>% add_trace(y = ~H3K27me3_absent, name = "H3K27me3 absent", color = I("grey"))
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb")
fig2
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 unbound | 933 | 190 |
| absent svbF7 unbound | 13651 | 5808 |
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 bound | 1120 | 0 |
| absent svbF7 bound | 13470 | 5456 |
pvalue_fixe = phyper(1120 - 1, 789, 20046 - 789, 14590)
pvalue_nonfixe = phyper(933 - 1, 1123, 20582 - 1123, 14584)
presence = c(1120,13470)
absence = c(0,5456)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me1_fixe_8_12 = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me1_fixe_8_12)
presence = c(933,13651)
absence = c(190,5808)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me1_nonfixe_8_12 = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me1_nonfixe_8_12)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 1.825385410^{-160} Celle du test de fisher pour les motifs non fixé est de 2.344941810^{-22}`
total_svbF7_unbound_H3K4me1 = 933 + 190
total_svbF7_bound_H3K4me1 = 1120 + 0
percent_svbf7_H3K4me1_unbound = round(100 * 933 / total_svbF7_unbound_H3K4me1, 2 )
percent_svbf7_unbound_without_H3K4me1 = round(100 * 190 / total_svbF7_unbound_H3K4me1, 2 )
percent_svbf7_H3K4me1_bound = round(100 * 1120 / total_svbF7_bound_H3K4me1, 2 )
percent_svbf7_bound_without_H3K4me1 = round(100 * 0 / total_svbF7_bound_H3K4me1, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me1_absent = c(percent_svbf7_bound_without_H3K4me1,percent_svbf7_unbound_without_H3K4me1)
H3K4me1_present = c(percent_svbf7_H3K4me1_bound,percent_svbf7_H3K4me1_unbound)
data_H3K4me1 = data.frame(etat_svb,H3K4me1_absent,H3K4me1_present)
datatable(data_H3K4me1,rownames = F,filter = "none",colnames = c("Regions without H3K4me1","Regions with H3K4me1" ))
fig4 = plot_ly(data_H3K4me1, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig4 = fig4 %>% add_trace(y = ~H3K4me1_absent, name = "H3K4me1 absent", color = I("grey"))
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me1 (embryo 8-12h) enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig4
fig4 = plot_ly(data_H3K4me1, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig4 = fig4 %>% add_trace(y = ~H3K4me1_absent, name = "H3K4me1 absent", color = I("grey"))
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me1 (embryo 8-12h) enrichment on svbF7 bound or not by Svb")
fig4
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 unbound | 725 | 398 |
| absent svbF7 unbound | 11878 | 7878 |
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 bound | 1012 | 0 |
| absent svbF7 bound | 11597 | 7718 |
pvalue_fixe = phyper(1012 - 1, 789, 20327 - 789, 12603)
pvalue_nonfixe = phyper(725 - 1, 1123, 20879 - 1123, 12603)
presence = c(1012,11597)
absence = c(0,7718)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me1_fixe_12_16 = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me1_fixe_12_16)
presence = c(725,11878)
absence = c(398,7878)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me1_nonfixe_12_16 = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me1_nonfixe_12_16)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 0.9983645
La pvalue du test de fisher pour les motifs fixé est de 1.6056910^{-217} Celle du test de fisher pour les motifs non fixé est de 0.0031876`
total_svbF7_unbound_H3K4me1 = 725 + 398
total_svbF7_bound_H3K4me1 = 1012 + 0
percent_svbf7_H3K4me1_unbound = round(100 * 725 / total_svbF7_unbound_H3K4me1, 2 )
percent_svbf7_unbound_without_H3K4me1 = round(100 * 398 / total_svbF7_unbound_H3K4me1, 2 )
percent_svbf7_H3K4me1_bound = round(100 * 1012 / total_svbF7_bound_H3K4me1, 2 )
percent_svbf7_bound_without_H3K4me1 = round(100 * 0 / total_svbF7_bound_H3K4me1, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me1_absent = c(percent_svbf7_bound_without_H3K4me1,percent_svbf7_unbound_without_H3K4me1)
H3K4me1_present = c(percent_svbf7_H3K4me1_bound,percent_svbf7_H3K4me1_unbound)
data_H3K4me1 = data.frame(etat_svb,H3K4me1_absent,H3K4me1_present)
datatable(data_H3K4me1,rownames = F,filter = "none",colnames = c("Regions without H3K4me1","Regions with H3K4me1" ))
fig3 = plot_ly(data_H3K4me1, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig3 = fig3 %>% add_trace(y = ~H3K4me1_absent, name = "H3K4me1 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 (embryo 12h-16h) enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig3
fig3 = plot_ly(data_H3K4me1, x = ~etat_svb,y = ~H3K4me1_present, type = "bar",name = "H3K4me1 present", color = I("orange"))
fig3 = fig3 %>% add_trace(y = ~H3K4me1_absent, name = "H3K4me1 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 (embryo 12h-16h) enrichment on svbF7 bound or not by Svb")
fig3
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 unbound | 296 | 827 |
| absent svbF7 unbound | 5876 | 12263 |
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 bound | 299 | 490 |
| absent svbF7 bound | 5873 | 12129 |
pvalue_fixe = phyper(299 - 1, 789, 18791 - 789, 6172)
pvalue_nonfixe = phyper(296 - 1, 789, 19262 - 1123, 6172)
presence = c(299,5873)
absence = c(490,12129)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me3_fixe_8_12 = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me3_fixe_8_12)
presence = c(296,586)
absence = c(398,7878)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me3_nonfixe_8_12 = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me3_nonfixe_8_12)
La pvalue du test de hypergéométrique pour les motifs fixé est de 0.9987244 Celle du test de hypergéométrique pour les motifs non fixé est de 0.9983399
La pvalue du test de fisher pour les motifs fixé est de 0.0022141 Celle du test de fisher pour les motifs non fixé est de 8.395345710^{-132}`
total_svbF7_unbound_H3K4me3 = 296 + 827
total_svbF7_bound_H3K4me3 = 299 + 490
percent_svbf7_H3K4me3_unbound = round(100 * 296 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_unbound_without_H3K4me3 = round(100 * 827 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_H3K4me3_bound = round(100 * 299 / total_svbF7_bound_H3K4me3, 2 )
percent_svbf7_bound_without_H3K4me3 = round(100 * 490 / total_svbF7_bound_H3K4me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me3_absent = c(percent_svbf7_bound_without_H3K4me3,percent_svbf7_unbound_without_H3K4me3)
H3K4me3_present = c(percent_svbf7_H3K4me3_bound,percent_svbf7_H3K4me3_unbound)
data_H3K4me3 = data.frame(etat_svb,H3K4me3_absent,H3K4me3_present)
datatable(data_H3K4me3,rownames = F,filter = "none",colnames = c("Regions without H3K4me3","Regions with H3K4me3" ))
fig3 = plot_ly(data_H3K4me3, x = ~etat_svb,y = ~H3K4me3_present, type = "bar",name = "H3K4me3 present" , color = I("pink"))
fig3 = fig3 %>% add_trace(y = ~H3K4me3_absent, name = "H3K4me3 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me3 (embryo 8-12h) enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig3
fig3 = plot_ly(data_H3K4me3, x = ~etat_svb,y = ~H3K4me3_present, type = "bar",name = "H3K4me3 present" , color = I("pink"))
fig3 = fig3 %>% add_trace(y = ~H3K4me3_absent, name = "H3K4me3 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me3 (embryo 8-12h) enrichment on svbF7 bound or not by Svb")
fig3
total_K4me1_8_12 = 14595
total_K4me3_8_12 = 6179
rapp_fixe_8_12 = round((contingence_H3K4me1_fixe_8_12[1,1]/total_K4me1_8_12) / (contingence_H3K4me3_fixe_8_12[1,1]/total_K4me3_8_12),2)
rapp_nonfixe_8_12 = round((contingence_H3K4me1_nonfixe[1,1]/total_K4me1_8_12) / (contingence_H3K4me3_nonfixe[1,1]/total_K4me3_8_12),2)
Il y a 1.59 fois de H3K4me1 que de H3K4me3 fixé.
Il y a 1.8 fois de H3K4me1 que de H3K4me3 non fixé.
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 unbound | 299 | 824 |
| absent svbF7 unbound | 6467 | 12309 |
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 bound | 340 | 449 |
| absent svbF7 bound | 6427 | 12182 |
pvalue_fixe = phyper(340 - 1, 789, 19398 - 789, 6767)
pvalue_nonfixe = phyper(299 - 1, 1123, 19899 - 1123, 6766)
presence = c(340,6427)
absence = c(449,12182)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me3_fixe_12_16 = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me3_fixe_12_16)
presence = c(299,6467)
absence = c(824,12309)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me3_nonfixe_12_16 = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me3_nonfixe_12_16)
La pvalue du test de hypergéométrique pour les motifs fixé est de 0.9999993 Celle du test de hypergéométrique pour les motifs non fixé est de 1.828087910^{-8}
La pvalue du test de fisher pour les motifs fixé est de 1.210093210^{-6} Celle du test de fisher pour les motifs non fixé est de 4.834952910^{-8}`
total_svbF7_unbound_H3K4me3 = 299 + 824
total_svbF7_bound_H3K4me3 = 340 + 449
percent_svbf7_H3K4me3_unbound = round(100 * 299 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_unbound_without_H3K4me3 = round(100 * 824 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_H3K4me3_bound = round(100 * 340 / total_svbF7_bound_H3K4me3, 2 )
percent_svbf7_bound_without_H3K4me3 = round(100 * 449 / total_svbF7_bound_H3K4me3, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K4me3_absent = c(percent_svbf7_bound_without_H3K4me3,percent_svbf7_unbound_without_H3K4me3)
H3K4me3_present = c(percent_svbf7_H3K4me3_bound,percent_svbf7_H3K4me3_unbound)
data_H3K4me3 = data.frame(etat_svb,H3K4me3_absent,H3K4me3_present)
datatable(data_H3K4me3,rownames = F,filter = "none",colnames = c("Regions without H3K4me3","Regions with H3K4me3" ))
fig3 = plot_ly(data_H3K4me3, x = ~etat_svb,y = ~H3K4me3_present, type = "bar",name = "H3K4me3 present", color = I("pink"))
fig3 = fig3 %>% add_trace(y = ~H3K4me3_absent, name = "H3K4me3 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me3 (embryo 12h-16h) enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig3
fig3 = plot_ly(data_H3K4me3, x = ~etat_svb,y = ~H3K4me3_present, type = "bar",name = "H3K4me3 present", color = I("pink"))
fig3 = fig3 %>% add_trace(y = ~H3K4me3_absent, name = "H3K4me3 absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me3 (embryo 12h-16h) enrichment on svbF7 bound or not by Svb")
fig3
total_K4me1_12_16 = 12613
total_K4me3_12_16 = 6775
rapp_fixe_12_16 = round((contingence_H3K4me1_fixe_8_12[1,1]/total_K4me1_12_16) / (contingence_H3K4me3_fixe_8_12[1,1]/total_K4me3_12_16),2)
rapp_nonfixe_12_16 = round((contingence_H3K4me1_nonfixe[1,1]/total_K4me1_12_16) / (contingence_H3K4me3_nonfixe[1,1]/total_K4me3_12_16),2)
Il y a 1.59 fois de H3K4me1 que de H3K4me3 fixé.
Il y a 1.8 fois de H3K4me1 que de H3K4me3 non fixé.
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 unbound | 515 | 608 |
| absent svbF7 unbound | 9616 | 9778 |
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 bound | 665 | 124 |
| absent svbF7 bound | 9467 | 9727 |
pvalue_fixe = phyper(665 - 1, 789, 19983 - 789, 10132)
pvalue_nonfixe = phyper(515 - 1, 1123, 20517 - 1123, 10131)
presence = c(665,9467)
absence = c(124,9727)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27ac_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27ac_fixe)
presence = c(515,9616)
absence = c(608,9778)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27ac_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27ac_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 0.0069799
La pvalue du test de fisher pour les motifs fixé est de 3.375421710^{-90} Celle du test de fisher pour les motifs non fixé est de 0.0153226`
total_svbF7_unbound_H3K27ac = 515 + 608
total_svbF7_bound_H3K27ac = 665 + 124
percent_svbf7_H3K27ac_unbound = round(100 * 515 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_unbound_without_H3K27ac = round(100 * 608 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_H3K27ac_bound = round(100 * 665 / total_svbF7_bound_H3K27ac, 2 )
percent_svbf7_bound_without_H3K27ac = round(100 * 124 / total_svbF7_bound_H3K27ac, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K27ac_absent = c(percent_svbf7_bound_without_H3K27ac,percent_svbf7_unbound_without_H3K27ac)
H3K27ac_present = c(percent_svbf7_H3K27ac_bound,percent_svbf7_H3K27ac_unbound)
data_H3K27ac = data.frame(etat_svb,H3K27ac_absent,H3K27ac_present)
datatable(data_H3K27ac,rownames = F,filter = "none",colnames = c("Regions without H3K27ac","Regions with H3K27ac" ))
fig3 = plot_ly(data_H3K27ac, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig3 = fig3 %>% add_trace(y = ~H3K27ac_absent, name = "H3K27ac absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K27ac (embryo 8-12h) enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig3
fig3 = plot_ly(data_H3K27ac, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig3 = fig3 %>% add_trace(y = ~H3K27ac_absent, name = "H3K27ac absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K27ac (embryo 8-12h) enrichment on svbF7 bound or not by Svb")
fig3
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 unbound | 500 | 623 |
| absent svbF7 unbound | 9959 | 9790 |
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 bound | 783 | 6 |
| absent svbF7 bound | 9676 | 9856 |
pvalue_fixe = phyper(783 - 1, 789, 20321 - 789, 10459)
pvalue_nonfixe = phyper(500 - 1, 1123, 20872 - 1123, 10459)
presence = c(665,9467)
absence = c(124,9727)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27ac_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27ac_fixe)
presence = c(515,9616)
absence = c(608,9778)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27ac_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27ac_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 5.152453810^{-5}
La pvalue du test de fisher pour les motifs fixé est de 3.375421710^{-90} Celle du test de fisher pour les motifs non fixé est de 0.0153226`
total_svbF7_unbound_H3K27ac = 500 + 623
total_svbF7_bound_H3K27ac = 783 + 6
percent_svbf7_H3K27ac_unbound = round(100 * 500 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_unbound_without_H3K27ac = round(100 * 623 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_H3K27ac_bound = round(100 * 783 / total_svbF7_bound_H3K27ac, 2 )
percent_svbf7_bound_without_H3K27ac = round(100 * 6 / total_svbF7_bound_H3K27ac, 2 )
etat_svb = c("svbF7_bound","svbF7_unbound")
H3K27ac_absent = c(percent_svbf7_bound_without_H3K27ac,percent_svbf7_unbound_without_H3K27ac)
H3K27ac_present = c(percent_svbf7_H3K27ac_bound,percent_svbf7_H3K27ac_unbound)
data_H3K27ac = data.frame(etat_svb,H3K27ac_absent,H3K27ac_present)
datatable(data_H3K27ac,rownames = F,filter = "none",colnames = c("Regions without H3K27ac","Regions with H3K27ac" ))
fig3 = plot_ly(data_H3K27ac, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig3 = fig3 %>% add_trace(y = ~H3K27ac_absent, name = "H3K27ac absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K27ac (embryo 8-12h) enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig3
data_H3K27ac = data.frame(etat_svb,H3K27ac_absent,H3K27ac_present)
datatable(data_H3K27ac,rownames = F,filter = "none",colnames = c("Regions without H3K27ac","Regions with H3K27ac" ))
fig3 = plot_ly(data_H3K27ac, x = ~etat_svb,y = ~H3K27ac_present, type = "bar",name = "H3K27ac present", color = I("blue"))
fig3 = fig3 %>% add_trace(y = ~H3K27ac_absent, name = "H3K27ac absent", color = I("grey"))
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K27ac (embryo 8-12h) enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig3
motif_svb_Bind_overlap_300 = findOverlapsOfPeaks(B1.peaks, ovoQ6_droso_gr_unique_300,svbF7_cons_gr_300)
makeVennDiagram(motif_svb_Bind_overlap_300,totalTest = 100,NameOfPeaks = c("SvbAct","ovoQ6", "svbF7"),fill=c("green","purple","orange"))
## $p.value
## SvbAct ovoQ6 svbF7 pval
## [1,] 0 1 1 NaN
## [2,] 1 0 1 NaN
## [3,] 1 1 0 NaN
##
## $vennCounts
## SvbAct ovoQ6 svbF7 Counts count.B1.peaks count.ovoQ6_droso_gr_unique_300
## [1,] 0 0 0 -64227 0 0
## [2,] 0 0 1 358 0 0
## [3,] 0 1 0 56902 0 56902
## [4,] 0 1 1 1645 0 2869
## [5,] 1 0 0 2179 2179 0
## [6,] 1 0 1 42 45 0
## [7,] 1 1 0 2919 2971 5012
## [8,] 1 1 1 282 317 740
## count.svbF7_cons_gr_300
## [1,] 0
## [2,] 358
## [3,] 0
## [4,] 1650
## [5,] 0
## [6,] 45
## [7,] 0
## [8,] 301
## attr(,"class")
## [1] "VennCounts"
ovoQ6_droso_svb_bind_overlap_300 = findOverlapsOfPeaks(B1.peaks,ovoQ6_droso_gr_unique_300)
makeVennDiagram(ovoQ6_droso_svb_bind_overlap_300,totalTest = 100,NameOfPeaks = c("SvbAct","ovoQ6"),fill=c("green","purple"))
## $p.value
## SvbAct ovoQ6 pval
## [1,] 1 1 NaN
##
## $vennCounts
## SvbAct ovoQ6 Counts count.B1.peaks count.ovoQ6_droso_gr_unique_300
## [1,] 0 0 -65207 0 0
## [2,] 0 1 59851 0 59851
## [3,] 1 0 2227 2227 0
## [4,] 1 1 3229 3285 5672
## attr(,"class")
## [1] "VennCounts"
svbF7_cons_gr_svb_bind_overlap_300 = findOverlapsOfPeaks(B1.peaks,svbF7_cons_gr_300)
makeVennDiagram(svbF7_cons_gr_svb_bind_overlap_300,totalTest = 100,NameOfPeaks = c("SvbAct", "svbF7"),fill=c("green","orange"))
## $p.value
## SvbAct svbF7 pval
## [1,] 1 1 NaN
##
## $vennCounts
## SvbAct svbF7 Counts count.B1.peaks count.svbF7_cons_gr_300
## [1,] 0 0 -7422 0 0
## [2,] 0 1 2029 0 2029
## [3,] 1 0 5187 5187 0
## [4,] 1 1 306 325 325
## attr(,"class")
## [1] "VennCounts"
svbF7_motifs_unbound_300 = as.data.frame(svbF7_cons_gr_svb_bind_overlap_300$peaklist$svbF7_cons_gr_300)
svbF7_motifs_bound_300 = as.data.frame(svbF7_cons_gr_svb_bind_overlap_300$peaklist$`B1.peaks///svbF7_cons_gr_300`)
ovoQ6_motifs_unbound_300 = as.data.frame(ovoQ6_droso_svb_bind_overlap_300$peaklist$ovoQ6_droso_gr_unique_300)
ovoQ6_motifs_bound_300 = as.data.frame(ovoQ6_droso_svb_bind_overlap_300$peaklist$`B1.peaks///ovoQ6_droso_gr_unique_300`)
motif_svb_Bind_overlap_300_low = findOverlapsOfPeaks(SvbACT.peaks_low, ovoQ6_droso_gr_unique_300,svbF7_cons_gr_300)
makeVennDiagram(motif_svb_Bind_overlap_300_low,totalTest = 100,NameOfPeaks = c("SvbAct","ovoQ6", "svbF7"),fill=c("green","purple","orange"))
## $p.value
## SvbAct ovoQ6 svbF7 pval
## [1,] 0 1 1 NaN
## [2,] 1 0 1 NaN
## [3,] 1 1 0 NaN
##
## $vennCounts
## SvbAct ovoQ6 svbF7 Counts count.SvbACT.peaks_low
## [1,] 0 0 0 -64446 0
## [2,] 0 0 1 351 0
## [3,] 0 1 0 55764 0
## [4,] 0 1 1 1603 0
## [5,] 1 0 0 2816 2816
## [6,] 1 0 1 49 51
## [7,] 1 1 0 3639 3703
## [8,] 1 1 1 324 368
## count.ovoQ6_droso_gr_unique_300 count.svbF7_cons_gr_300
## [1,] 0 0
## [2,] 0 351
## [3,] 55764 0
## [4,] 2781 1608
## [5,] 0 0
## [6,] 0 52
## [7,] 6133 0
## [8,] 845 343
## attr(,"class")
## [1] "VennCounts"
ovoQ6_droso_svb_bind_overlap_300_low = findOverlapsOfPeaks(SvbACT.peaks_low,ovoQ6_droso_gr_unique_300)
makeVennDiagram(ovoQ6_droso_svb_bind_overlap_300_low,totalTest = 100,NameOfPeaks = c("SvbAct","ovoQ6"),fill=c("green","purple"))
## $p.value
## SvbAct ovoQ6 pval
## [1,] 1 1 NaN
##
## $vennCounts
## SvbAct ovoQ6 Counts count.SvbACT.peaks_low count.ovoQ6_droso_gr_unique_300
## [1,] 0 0 -65396 0 0
## [2,] 0 1 58624 0 58624
## [3,] 1 0 2870 2870 0
## [4,] 1 1 4002 4068 6899
## attr(,"class")
## [1] "VennCounts"
svbF7_cons_gr_svb_bind_overlap_300_low = findOverlapsOfPeaks(SvbACT.peaks_low,svbF7_cons_gr_300)
makeVennDiagram(svbF7_cons_gr_svb_bind_overlap_300_low,totalTest = 100,NameOfPeaks = c("SvbAct", "svbF7"),fill=c("green","orange"))
## $p.value
## SvbAct svbF7 pval
## [1,] 1 1 NaN
##
## $vennCounts
## SvbAct svbF7 Counts count.SvbACT.peaks_low count.svbF7_cons_gr_300
## [1,] 0 0 -8808 0 0
## [2,] 0 1 1986 0 1986
## [3,] 1 0 6573 6573 0
## [4,] 1 1 349 365 368
## attr(,"class")
## [1] "VennCounts"
svbF7_motifs_unbound_300_low = as.data.frame(svbF7_cons_gr_svb_bind_overlap_300_low$peaklist$svbF7_cons_gr_300)
svbF7_motifs_bound_300_low = as.data.frame(svbF7_cons_gr_svb_bind_overlap_300_low$peaklist$`SvbACT.peaks_low///svbF7_cons_gr_300`)
ovoQ6_motifs_unbound_300_low = as.data.frame(ovoQ6_droso_svb_bind_overlap_300_low$peaklist$ovoQ6_droso_gr_unique_300)
ovoQ6_motifs_bound_300_low = as.data.frame(ovoQ6_droso_svb_bind_overlap_300_low$peaklist$`SvbACT.peaks_low///ovoQ6_droso_gr_unique_300`)
motif_svb_Bind_overlap_300_embryo = findOverlapsOfPeaks(SvbACT.peaks_embryo, ovoQ6_droso_gr_unique_300,svbF7_cons_gr_300)
makeVennDiagram(motif_svb_Bind_overlap_300_embryo,totalTest = 100,NameOfPeaks = c("SvbAct","ovoQ6", "svbF7"),fill=c("green","purple","orange"))
## $p.value
## SvbAct ovoQ6 svbF7 pval
## [1,] 0 1 1 NaN
## [2,] 1 0 1 NaN
## [3,] 1 1 0 NaN
##
## $vennCounts
## SvbAct ovoQ6 svbF7 Counts count.SvbACT.peaks_embryo
## [1,] 0 0 0 -66627 0
## [2,] 0 0 1 348 0
## [3,] 0 1 0 56218 0
## [4,] 0 1 1 1568 0
## [5,] 1 0 0 4392 4392
## [6,] 1 0 1 50 53
## [7,] 1 1 0 3796 3858
## [8,] 1 1 1 355 403
## count.ovoQ6_droso_gr_unique_300 count.svbF7_cons_gr_300
## [1,] 0 0
## [2,] 0 348
## [3,] 56218 0
## [4,] 2734 1572
## [5,] 0 0
## [6,] 0 52
## [7,] 5686 0
## [8,] 885 382
## attr(,"class")
## [1] "VennCounts"
ovoQ6_droso_svb_bind_overlap_300_embryo = findOverlapsOfPeaks(SvbACT.peaks_embryo,ovoQ6_droso_gr_unique_300)
makeVennDiagram(ovoQ6_droso_svb_bind_overlap_300_embryo,totalTest = 100,NameOfPeaks = c("SvbAct","ovoQ6"),fill=c("green","purple"))
## $p.value
## SvbAct ovoQ6 pval
## [1,] 1 1 NaN
##
## $vennCounts
## SvbAct ovoQ6 Counts count.SvbACT.peaks_embryo
## [1,] 0 0 -67606 0
## [2,] 0 1 59071 0
## [3,] 1 0 4446 4446
## [4,] 1 1 4189 4260
## count.ovoQ6_droso_gr_unique_300
## [1,] 0
## [2,] 59071
## [3,] 0
## [4,] 6452
## attr(,"class")
## [1] "VennCounts"
svbF7_cons_gr_svb_bind_overlap_300_embryo = findOverlapsOfPeaks(SvbACT.peaks_embryo,svbF7_cons_gr_300)
makeVennDiagram(svbF7_cons_gr_svb_bind_overlap_300_embryo,totalTest = 100,NameOfPeaks = c("SvbAct", "svbF7"),fill=c("green","orange"))
## $p.value
## SvbAct svbF7 pval
## [1,] 1 1 NaN
##
## $vennCounts
## SvbAct svbF7 Counts count.SvbACT.peaks_embryo count.svbF7_cons_gr_300
## [1,] 0 0 -10537 0 0
## [2,] 0 1 1959 0 1959
## [3,] 1 0 8307 8307 0
## [4,] 1 1 371 399 395
## attr(,"class")
## [1] "VennCounts"
svbF7_motifs_unbound_300_embryo = as.data.frame(svbF7_cons_gr_svb_bind_overlap_300_embryo$peaklist$svbF7_cons_gr_300)
svbF7_motifs_bound_300_embryo = as.data.frame(svbF7_cons_gr_svb_bind_overlap_300_embryo$peaklist$`SvbACT.peaks_embryo///svbF7_cons_gr_300`)
ovoQ6_motifs_unbound_300_embryo = as.data.frame(ovoQ6_droso_svb_bind_overlap_300_embryo$peaklist$ovoQ6_droso_gr_unique_300)
ovoQ6_motifs_bound_300_embryo = as.data.frame(ovoQ6_droso_svb_bind_overlap_300_embryo$peaklist$`SvbACT.peaks_embryo///ovoQ6_droso_gr_unique_300`)
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 unbound | 167 | 1764 |
| absent svbF7 unbound | 4981 | 24285 |
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 bound | 174 | 127 |
| absent svbF7 bound | 4979 | 25028 |
pvalue_fixe = phyper(174 - 1, 301, 30308 - 301, 5153)
pvalue_nonfixe = phyper(167 - 1, 1931, 31197 - 1931, 5148)
presence = c(174,4979)
absence = c(127,25028)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27ac_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27ac_fixe)
presence = c(167,4981)
absence = c(1764,24285)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27ac_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27ac_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 1.632559610^{-25}
La pvalue du test de fisher pour les motifs fixé est de 6.336471410^{-58} Celle du test de fisher pour les motifs non fixé est de 7.33482810^{-25}`
total_svbF7_unbound_H3K27ac = 117 + 1773
total_svbF7_bound_H3K27ac = 214 + 128
percent_svbf7_H3K27ac_unbound = round(100 * 117 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_unbound_without_H3K27ac = round(100 * 1773 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_H3K27ac_bound = round(100 * 214 / total_svbF7_bound_H3K27ac, 2 )
percent_svbf7_bound_without_H3K27ac = round(100 * 128 / total_svbF7_bound_H3K27ac, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K27ac_absent = c(percent_svbf7_bound_without_H3K27ac,percent_svbf7_unbound_without_H3K27ac)
H3K27ac_present = c(percent_svbf7_H3K27ac_bound,percent_svbf7_H3K27ac_unbound)
data_H3K27ac = data.frame(etat_svb,H3K27ac_absent,H3K27ac_present)
datatable(data_H3K27ac,rownames = F,filter = "none",colnames = c("Regions without H3K27ac","Regions with H3K27ac" ))
fig1 = plot_ly(data_H3K27ac, x = ~etat_svb,y = ~H3K27ac_absent, type = "bar",name = "H3K27ac absent")
fig1 = fig1 %>% add_trace(y = ~H3K27ac_present, name = "H3K27ac present")
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb")
fig1
fig1 = plot_ly(data_H3K27ac, x = ~etat_svb,y = ~H3K27ac_absent, type = "bar",name = "H3K27ac absent")
fig1 = fig1 %>% add_trace(y = ~H3K27ac_present, name = "H3K27ac present")
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig1
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 unbound | 736 | 1195 |
| absent svbF7 unbound | 12699 | 49770 |
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 bound | 48 | 253 |
| absent svbF7 bound | 13390 | 46987 |
pvalue_fixe = phyper(48 - 1, 301, 60678 - 301, 13438)
pvalue_nonfixe =phyper(736 - 1, 1931, 64400 - 1931, 13435)
presence = c(48,13390)
absence = c(253,46987)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27me3_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27me3_fixe)
presence = c(736,12699)
absence = c(1195,49770)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27me3_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27ac_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 0.0029026 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 0.0081554 Celle du test de fisher pour les motifs non fixé est de 7.33482810^{-25}`
total_svbF7_unbound_H3K27me3 = 736 + 1195
total_svbF7_bound_H3K27me3 = 48 + 253
percent_svbf7_H3K27me3_unbound = round(100 * 736 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_unbound_without_H3K27me3 = round(100 * 1195 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_H3K27me3_bound = round(100 * 48 / total_svbF7_bound_H3K27me3, 2 )
percent_svbf7_bound_without_H3K27me3 = round(100 * 253 / total_svbF7_bound_H3K27me3, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K27me3_absent = c(percent_svbf7_bound_without_H3K27me3,percent_svbf7_unbound_without_H3K27me3)
H3K27me3_present = c(percent_svbf7_H3K27me3_bound,percent_svbf7_H3K27me3_unbound)
data_H3K27me3 = data.frame(etat_svb,H3K27me3_absent,H3K27me3_present)
datatable(data_H3K27me3,rownames = F,filter = "none",colnames = c("Regions without H3K27me3","Regions with H3K27me3" ))
fig2 = plot_ly(data_H3K27me3, x = ~etat_svb,y = ~H3K27me3_absent, type = "bar",name = "H3K27me3 absent")
fig2 = fig2 %>% add_trace(y = ~H3K27me3_present, name = "H3K27me3 present")
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb")
fig2
fig2 = plot_ly(data_H3K27me3, x = ~etat_svb,y = ~H3K27me3_absent, type = "bar",name = "H3K27me3 absent")
fig2 = fig2 %>% add_trace(y = ~H3K27me3_present, name = "H3K27me3 present")
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig2
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 unbound | 321 | 1610 |
| absent svbF7 unbound | 8445 | 31802 |
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 bound | 211 | 90 |
| absent svbF7 bound | 8561 | 31674 |
pvalue_fixe = phyper(321 - 1, 1931, 42178 - 1931, 8766)
pvalue_nonfixe = phyper(211 - 1, 301, 40536 - 301, 8772)
presence = c(211,8561)
absence = c(90,31674)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me1_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me1_fixe)
presence = c(736,12699)
absence = c(1195,49770)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me1_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me1_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 9.840557510^{-7} Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 1.068099710^{-72} Celle du test de fisher pour les motifs non fixé est de 1.97416510^{-69}`
total_svbF7_unbound_H3K4me1 = 321 + 1610
total_svbF7_bound_H3K4me1 = 211 + 90
percent_svbf7_H3K4me1_unbound = round(100 * 321 / total_svbF7_unbound_H3K4me1, 2 )
percent_svbf7_unbound_without_H3K4me1 = round(100 * 1610 / total_svbF7_unbound_H3K4me1, 2 )
percent_svbf7_H3K4me1_bound = round(100 * 211 / total_svbF7_bound_H3K4me1, 2 )
percent_svbf7_bound_without_H3K4me1 = round(100 * 90 / total_svbF7_bound_H3K4me1, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K4me1_absent = c(percent_svbf7_bound_without_H3K4me1,percent_svbf7_unbound_without_H3K4me1)
H3K4me1_present = c(percent_svbf7_H3K4me1_bound,percent_svbf7_H3K4me1_unbound)
data_H3K4me1 = data.frame(etat_svb,H3K4me1_absent,H3K4me1_present)
datatable(data_H3K4me1,rownames = F,filter = "none",colnames = c("Regions without H3K4me1","Regions with H3K4me1" ))
fig3 = plot_ly(data_H3K4me1, x = ~etat_svb,y = ~H3K4me1_absent, type = "bar",name = "H3K4me1 absent")
fig3 = fig3 %>% add_trace(y = ~H3K4me1_present, name = "H3K4me1 present")
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb")
fig3
fig3 = plot_ly(data_H3K4me1, x = ~etat_svb,y = ~H3K4me1_absent, type = "bar",name = "H3K4me1 absent")
fig3 = fig3 %>% add_trace(y = ~H3K4me1_present, name = "H3K4me1 present")
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig3
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 unbound | 69 | 1862 |
| absent svbF7 unbound | 4738 | 46371 |
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 bound | 109 | 192 |
| absent svbF7 bound | 4699 | 45486 |
pvalue_fixe = phyper(109 - 1, 301, 50486 - 301, 4808)
pvalue_nonfixe = phyper(69 - 1, 1931, 53040 - 1931, 4807)
presence = c(109,4699)
absence = c(192,45486)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me3_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me3_fixe)
presence = c(69,4738)
absence = c(1195,49770)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me3_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me3_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 2.268887910^{-22}
La pvalue du test de fisher pour les motifs fixé est de 2.306606710^{-36} Celle du test de fisher pour les motifs non fixé est de 2.425768410^{-5}`
total_svbF7_unbound_H3K4me3 = 69 + 1862
total_svbF7_bound_H3K4me3 = 109 + 192
percent_svbf7_H3K4me3_unbound = round(100 * 69 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_unbound_without_H3K4me3 = round(100 * 1862 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_H3K4me3_bound = round(100 * 109 / total_svbF7_bound_H3K4me3, 2 )
percent_svbf7_bound_without_H3K4me3 = round(100 * 192 / total_svbF7_bound_H3K4me3, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K4me3_absent = c(percent_svbf7_bound_without_H3K4me3,percent_svbf7_unbound_without_H3K4me3)
H3K4me3_present = c(percent_svbf7_H3K4me3_bound,percent_svbf7_H3K4me3_unbound)
data_H3K4me3 = data.frame(etat_svb,H3K4me3_absent,H3K4me3_present)
datatable(data_H3K4me3,rownames = F,filter = "none",colnames = c("Regions without H3K4me3","Regions with H3K4me3" ))
fig4 = plot_ly(data_H3K4me3, x = ~etat_svb,y = ~H3K4me3_absent, type = "bar",name = "H3K4me3 absent")
fig4 = fig4 %>% add_trace(y = ~H3K4me1_present, name = "H3K4me3 present")
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb")
fig4
fig4 = plot_ly(data_H3K4me3, x = ~etat_svb,y = ~H3K4me3_absent, type = "bar",name = "H3K4me3 absent")
fig4 = fig4 %>% add_trace(y = ~H3K4me3_present, name = "H3K4me3 present")
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig4
rapp_fixe = round((contingence_H3K4me1_fixe[1,1]/total_K4me1_S2) / (contingence_H3K4me3_fixe[1,1]/total_K4me3_S2),2)
rapp_nonfixe = round((contingence_H3K4me1_nonfixe[1,1]/total_K4me1_S2) / (contingence_H3K4me3_nonfixe[1,1]/total_K4me3_S2),2)
Il y a 1.06 fois de H3K4me1 que de H3K4me3 fixé.
Il y a 5.84 fois de H3K4me1 que de H3K4me3 non fixé.
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 unbound | 152 | 1738 |
| absent svbF7 unbound | 4996 | 24312 |
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 bound | 190 | 152 |
| absent svbF7 bound | 4963 | 24886 |
pvalue_fixe = phyper(1190 - 1, 343, 30191 - 342, 5153)
pvalue_nonfixe = phyper(152 - 1, 1890, 31198 - 1890, 5148)
presence = c(190,4963)
absence = c(152,24886)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27ac_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27ac_fixe)
presence = c(152,4996)
absence = c(1738,24312)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27ac_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27ac_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 4.446086610^{-29}
La pvalue du test de fisher pour les motifs fixé est de 4.135509110^{-59} Celle du test de fisher pour les motifs non fixé est de 2.014332510^{-28}`
total_svbF7_unbound_H3K27ac = 122 + 1738
total_svbF7_bound_H3K27ac = 190 + 152
percent_svbf7_H3K27ac_unbound = round(100 * 122 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_unbound_without_H3K27ac = round(100 * 1738 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_H3K27ac_bound = round(100 * 190 / total_svbF7_bound_H3K27ac, 2 )
percent_svbf7_bound_without_H3K27ac = round(100 * 157 / total_svbF7_bound_H3K27ac, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K27ac_absent = c(percent_svbf7_bound_without_H3K27ac,percent_svbf7_unbound_without_H3K27ac)
H3K27ac_present = c(percent_svbf7_H3K27ac_bound,percent_svbf7_H3K27ac_unbound)
data_H3K27ac = data.frame(etat_svb,H3K27ac_absent,H3K27ac_present)
datatable(data_H3K27ac,rownames = F,filter = "none",colnames = c("Regions without H3K27ac","Regions with H3K27ac" ))
fig1 = plot_ly(data_H3K27ac, x = ~etat_svb,y = ~H3K27ac_absent, type = "bar",name = "H3K27ac absent")
fig1 = fig1 %>% add_trace(y = ~H3K27ac_present, name = "H3K27ac present")
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb")
fig1
fig1 = plot_ly(data_H3K27ac, x = ~etat_svb,y = ~H3K27ac_absent, type = "bar",name = "H3K27ac absent")
fig1 = fig1 %>% add_trace(y = ~H3K27ac_present, name = "H3K27ac present")
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig1
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 unbound | 728 | 1162 |
| absent svbF7 unbound | 12707 | 49806 |
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 bound | 57 | 285 |
| absent svbF7 bound | 13381 | 46489 |
pvalue_fixe = phyper(57 - 1, 342, 60212 - 342, 13438)
pvalue_nonfixe = phyper(728 - 1, 1890, 64403 - 1890, 13435)
presence = c(57,13381)
absence = c(285,46489)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27me3_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27me3_fixe)
presence = c(7282,12707)
absence = c(1162,49806)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27me3_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27me3_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 0.0039024 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 0.0110048 Celle du test de fisher pour les motifs non fixé est de 0`
total_svbF7_unbound_H3K27me3 = 728 + 1162
total_svbF7_bound_H3K27me3 = 57 + 285
percent_svbf7_H3K27me3_unbound = round(100 * 728 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_unbound_without_H3K27me3 = round(100 * 1162 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_H3K27me3_bound = round(100 * 57 / total_svbF7_bound_H3K27me3, 2 )
percent_svbf7_bound_without_H3K27me3 = round(100 * 285 / total_svbF7_bound_H3K27me3, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K27me3_absent = c(percent_svbf7_bound_without_H3K27me3,percent_svbf7_unbound_without_H3K27me3)
H3K27me3_present = c(percent_svbf7_H3K27me3_bound,percent_svbf7_H3K27me3_unbound)
data_H3K27me3 = data.frame(etat_svb,H3K27me3_absent,H3K27me3_present)
datatable(data_H3K27me3,rownames = F,filter = "none",colnames = c("Regions without H3K27me3","Regions with H3K27me3" ))
fig2 = plot_ly(data_H3K27me3, x = ~etat_svb,y = ~H3K27me3_absent, type = "bar",name = "H3K27me3 absent")
fig2 = fig2 %>% add_trace(y = ~H3K27me3_present, name = "H3K27me3 present")
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb")
fig2
fig2 = plot_ly(data_H3K27me3, x = ~etat_svb,y = ~H3K27me3_absent, type = "bar",name = "H3K27me3 absent")
fig2 = fig2 %>% add_trace(y = ~H3K27me3_present, name = "H3K27me3 present")
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig2
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 unbound | 302 | 1588 |
| absent svbF7 unbound | 8464 | 31826 |
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 bound | 232 | 110 |
| absent svbF7 bound | 8540 | 31446 |
pvalue_fixe = phyper(232 - 1, 342, 40328 - 342, 8772)
pvalue_nonfixe = phyper(302 - 1, 1890, 42180 - 1890, 8766)
presence = c(232,8540)
absence = c(110,31446)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me1_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me1_fixe)
presence = c(302,8464)
absence = c(1588,31826)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me1_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me1_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 2.482721810^{-8}
La pvalue du test de fisher pour les motifs fixé est de 6.355519110^{-75} Celle du test de fisher pour les motifs non fixé est de 6.574769710^{-8}`
total_svbF7_unbound_H3K4me1 = 302 + 1588
total_svbF7_bound_H3K4me1 = 232 + 110
percent_svbf7_H3K4me1_unbound = round(100 * 321 / total_svbF7_unbound_H3K4me1, 2 )
percent_svbf7_unbound_without_H3K4me1 = round(100 * 1588 / total_svbF7_unbound_H3K4me1, 2 )
percent_svbf7_H3K4me1_bound = round(100 * 232 / total_svbF7_bound_H3K4me1, 2 )
percent_svbf7_bound_without_H3K4me1 = round(100 * 110 / total_svbF7_bound_H3K4me1, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K4me1_absent = c(percent_svbf7_bound_without_H3K4me1,percent_svbf7_unbound_without_H3K4me1)
H3K4me1_present = c(percent_svbf7_H3K4me1_bound,percent_svbf7_H3K4me1_unbound)
data_H3K4me1 = data.frame(etat_svb,H3K4me1_absent,H3K4me1_present)
datatable(data_H3K4me1,rownames = F,filter = "none",colnames = c("Regions without H3K4me1","Regions with H3K4me1" ))
fig3 = plot_ly(data_H3K4me1, x = ~etat_svb,y = ~H3K4me1_absent, type = "bar",name = "H3K4me1 absent")
fig3 = fig3 %>% add_trace(y = ~H3K4me1_present, name = "H3K4me1 present")
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb")
fig3
fig3 = plot_ly(data_H3K4me1, x = ~etat_svb,y = ~H3K4me1_absent, type = "bar",name = "H3K4me1 absent")
fig3 = fig3 %>% add_trace(y = ~H3K4me1_present, name = "H3K4me1 present")
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig3
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 unbound | 60 | 1830 |
| absent svbF7 unbound | 4747 | 46405 |
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 bound | 119 | 223 |
| absent svbF7 bound | 4689 | 45133 |
pvalue_fixe = phyper(119 - 1, 342, 50164 - 342, 4808)
pvalue_nonfixe = phyper(728 - 1, 1890, 64403 - 1890, 13435)
presence = c(57,13381)
absence = c(285,46489)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me3_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me3_fixe)
presence = c(7282,12707)
absence = c(1162,49806)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me3_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me3_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 0.0110048 Celle du test de fisher pour les motifs non fixé est de 0`
total_svbF7_unbound_H3K4me3 = 121 + 1206
total_svbF7_bound_H3K4me3 = 388 + 161
percent_svbf7_H3K4me3_unbound = round(100 * 121 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_unbound_without_H3K4me3 = round(100 * 1206 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_H3K4me3_bound = round(100 * 388 / total_svbF7_bound_H3K4me3, 2 )
percent_svbf7_bound_without_H3K4me3 = round(100 * 161 / total_svbF7_bound_H3K4me3, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K4me3_absent = c(percent_svbf7_bound_without_H3K4me3,percent_svbf7_unbound_without_H3K4me3)
H3K4me3_present = c(percent_svbf7_H3K4me3_bound,percent_svbf7_H3K4me3_unbound)
data_H3K4me3 = data.frame(etat_svb,H3K4me3_absent,H3K4me3_present)
datatable(data_H3K4me3,rownames = F,filter = "none",colnames = c("Regions without H3K4me3","Regions with H3K4me3" ))
fig4 = plot_ly(data_H3K4me3, x = ~etat_svb,y = ~H3K4me3_absent, type = "bar",name = "H3K4me3 absent")
fig4 = fig4 %>% add_trace(y = ~H3K4me1_present, name = "H3K4me3 present")
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb")
fig4
fig4 = plot_ly(data_H3K4me3, x = ~etat_svb,y = ~H3K4me3_absent, type = "bar",name = "H3K4me3 absent")
fig4 = fig4 %>% add_trace(y = ~H3K4me3_present, name = "H3K4me3 present")
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig4
rapp_fixe = round((contingence_H3K4me1_fixe[1,1]/total_K4me1_S2) / (contingence_H3K4me3_fixe[1,1]/total_K4me3_S2),2)
rapp_nonfixe = round((contingence_H3K4me1_nonfixe[1,1]/total_K4me1_S2) / (contingence_H3K4me3_nonfixe[1,1]/total_K4me3_S2),2)
Il y a 2.23 fois de H3K4me1 que de H3K4me3 fixé.
Il y a 0.02 fois de H3K4me1 que de H3K4me3 non fixé.
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 unbound | 196 | 1670 |
| absent svbF7 unbound | 9935 | 107649 |
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 bound | 65 | 303 |
| absent svbF7 bound | 10067 | 98675 |
pvalue_fixe = phyper(65 - 1, 368, 109110 - 368, 10132)
pvalue_nonfixe = phyper(196 - 1, 1866, 119450 - 1866, 10131)
presence = c(65,10067)
absence = c(303,98675)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27ac_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27ac_fixe)
presence = c(196,9935)
absence = c(1670,107649)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H327ac_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H327ac_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 0.9999996 Celle du test de hypergéométrique pour les motifs non fixé est de 0.9987769
La pvalue du test de fisher pour les motifs fixé est de 5.111577810^{-7} Celle du test de fisher pour les motifs non fixé est de 0.0022066`
total_svbF7_unbound_H3K27ac = 196 + 1670
total_svbF7_bound_H3K27ac = 65 + 303
percent_svbf7_H3K27ac_unbound = round(100 * 196 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_unbound_without_H3K27ac = round(100 * 1670 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_H3K27ac_bound = round(100 * 65 / total_svbF7_bound_H3K27ac, 2 )
percent_svbf7_bound_without_H3K27ac = round(100 * 303 / total_svbF7_bound_H3K27ac, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K27ac_absent = c(percent_svbf7_bound_without_H3K27ac,percent_svbf7_unbound_without_H3K27ac)
H3K27ac_present = c(percent_svbf7_H3K27ac_bound,percent_svbf7_H3K27ac_unbound)
data_H3K27ac = data.frame(etat_svb,H3K27ac_absent,H3K27ac_present)
datatable(data_H3K27ac,rownames = F,filter = "none",colnames = c("Regions without H3K27ac","Regions with H3K27ac" ))
fig1 = plot_ly(data_H3K27ac, x = ~etat_svb,y = ~H3K27ac_absent, type = "bar",name = "H3K27ac absent")
fig1 = fig1 %>% add_trace(y = ~H3K27ac_present, name = "H3K27ac present")
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb")
fig1
fig1 = plot_ly(data_H3K27ac, x = ~etat_svb,y = ~H3K27ac_absent, type = "bar",name = "H3K27ac absent")
fig1 = fig1 %>% add_trace(y = ~H3K27ac_present, name = "H3K27ac present")
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig1
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 unbound | 255 | 1611 |
| absent svbF7 unbound | 6507 | 80721 |
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 bound | 38 | 330 |
| absent svbF7 bound | 6724 | 76125 |
pvalue_fixe = phyper(38 - 1, 368, 83217 - 368 , 6762)
pvalue_nonfixe = phyper(255 - 1, 1866, 89094 - 1866, 6762)
presence = c(30,6724)
absence = c(330,76125)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27me3_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27me3_fixe)
presence = c(255,6507)
absence = c(1611,80721)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27me3_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27me3_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 0.9232816 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 0.8466164 Celle du test de fisher pour les motifs non fixé est de 8.067370810^{-20}`
total_svbF7_unbound_H3K27me3 = 255 + 1611
total_svbF7_bound_H3K27me3 = 38 + 330
percent_svbf7_H3K27me3_unbound = round(100 * 255 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_unbound_without_H3K27me3 = round(100 * 1611/ total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_H3K27me3_bound = round(100 * 38 / total_svbF7_bound_H3K27me3, 2 )
percent_svbf7_bound_without_H3K27me3 = round(100 * 330 / total_svbF7_bound_H3K27me3, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K27me3_absent = c(percent_svbf7_bound_without_H3K27me3,percent_svbf7_unbound_without_H3K27me3)
H3K27me3_present = c(percent_svbf7_H3K27me3_bound,percent_svbf7_H3K27me3_unbound)
data_H3K27me3 = data.frame(etat_svb,H3K27me3_absent,H3K27me3_present)
datatable(data_H3K27me3,rownames = F,filter = "none",colnames = c("Regions without H3K27me3","Regions with H3K27me3" ))
fig2 = plot_ly(data_H3K27me3, x = ~etat_svb,y = ~H3K27me3_absent, type = "bar",name = "H3K27me3 absent")
fig2 = fig2 %>% add_trace(y = ~H3K27me3_present, name = "H3K27me3 present")
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb")
fig2
fig2 = plot_ly(data_H3K27me3, x = ~etat_svb,y = ~H3K27me3_absent, type = "bar",name = "H3K27me3 absent")
fig2 = fig2 %>% add_trace(y = ~H3K27me3_present, name = "H3K27me3 present")
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig2
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 unbound | 336 | 1530 |
| absent svbF7 unbound | 14247 | 105586 |
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 bound | 104 | 264 |
| absent svbF7 bound | 14483 | 96147 |
pvalue_fixe = phyper(336 - 1, 368, 121699 - 368, 14583)
pvalue_nonfixe = phyper(104 - 1, 1866, 110998 - 1866, 14587)
presence = c(104,14483)
absence = c(264,96147)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me1_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me1_fixe)
presence = c(336,14247)
absence = c(1530,105586)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me1_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me1_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 7.334647710^{-28}
La pvalue du test de fisher pour les motifs fixé est de 2.453873510^{-14} Celle du test de fisher pour les motifs non fixé est de 2.628965710^{-14}`
total_svbF7_unbound_H3K4me1 = 336 + 1530
total_svbF7_bound_H3K4me1 = 104 + 264
percent_svbf7_H3K4me1_unbound = round(100 * 336 / total_svbF7_unbound_H3K4me1, 2 )
percent_svbf7_unbound_without_H3K4me1 = round(100 * 1530 / total_svbF7_unbound_H3K4me1, 2 )
percent_svbf7_H3K4me1_bound = round(100 * 104 / total_svbF7_bound_H3K4me1, 2 )
percent_svbf7_bound_without_H3K4me1 = round(100 * 264 / total_svbF7_bound_H3K4me1, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K4me1_absent = c(percent_svbf7_bound_without_H3K4me1,percent_svbf7_unbound_without_H3K4me1)
H3K4me1_present = c(percent_svbf7_H3K4me1_bound,percent_svbf7_H3K4me1_unbound)
data_H3K4me1 = data.frame(etat_svb,H3K4me1_absent,H3K4me1_present)
datatable(data_H3K4me1,rownames = F,filter = "none",colnames = c("Regions without H3K4me1","Regions with H3K4me1" ))
fig3 = plot_ly(data_H3K4me1, x = ~etat_svb,y = ~H3K4me1_absent, type = "bar",name = "H3K4me1 absent")
fig3 = fig3 %>% add_trace(y = ~H3K4me1_present, name = "H3K4me1 present")
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb")
fig3
fig3 = plot_ly(data_H3K4me1, x = ~etat_svb,y = ~H3K4me1_absent, type = "bar",name = "H3K4me1 absent")
fig3 = fig3 %>% add_trace(y = ~H3K4me1_present, name = "H3K4me1 present")
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig3
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 unbound | 114 | 1752 |
| absent svbF7 unbound | 6058 | 78680 |
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 bound | 48 | 320 |
| absent svbF7 bound | 6124 | 74548 |
pvalue_fixe = phyper(48 - 1, 368, 81040 - 368, 6172)
pvalue_nonfixe = phyper(114 - 1, 1866, 866004 - 1866, 6172)
presence = c(48,6124)
absence = c(320,74548)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me3_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me3_fixe)
presence = c(114,6058)
absence = c(1752,78680)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me3_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me3_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 0.999802 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 3.404928210^{-4} Celle du test de fisher pour les motifs non fixé est de 0.0921426`
total_svbF7_unbound_H3K4me3 = 114 + 1752
total_svbF7_bound_H3K4me3 = 48 + 320
percent_svbf7_H3K4me3_unbound = round(100 * 114 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_unbound_without_H3K4me3 = round(100 * 1752 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_H3K4me3_bound = round(100 * 48 / total_svbF7_bound_H3K4me3, 2 )
percent_svbf7_bound_without_H3K4me3 = round(100 * 320 / total_svbF7_bound_H3K4me3, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K4me3_absent = c(percent_svbf7_bound_without_H3K4me3,percent_svbf7_unbound_without_H3K4me3)
H3K4me3_present = c(percent_svbf7_H3K4me3_bound,percent_svbf7_H3K4me3_unbound)
data_H3K4me3 = data.frame(etat_svb,H3K4me3_absent,H3K4me3_present)
datatable(data_H3K4me3,rownames = F,filter = "none",colnames = c("Regions without H3K4me3","Regions with H3K4me3" ))
fig4 = plot_ly(data_H3K4me3, x = ~etat_svb,y = ~H3K4me3_absent, type = "bar",name = "H3K4me3 absent")
fig4 = fig4 %>% add_trace(y = ~H3K4me1_present, name = "H3K4me3 present")
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb")
fig4
fig4 = plot_ly(data_H3K4me3, x = ~etat_svb,y = ~H3K4me3_absent, type = "bar",name = "H3K4me3 absent")
fig4 = fig4 %>% add_trace(y = ~H3K4me3_present, name = "H3K4me3 present")
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig4
rapp_fixe = round((contingence_H3K4me1_fixe[1,1]/total_K4me1_8_12) / (contingence_H3K4me3_fixe[1,1]/total_K4me3_8_12),2)
rapp_nonfixe = round((contingence_H3K4me1_nonfixe[1,1]/total_K4me1_8_12) / (contingence_H3K4me3_nonfixe[1,1]/total_K4me3_8_12),2)
Il y a 0.92 fois de H3K4me1 que de H3K4me3 fixé.
Il y a 1.25 fois de H3K4me1 que de H3K4me3 non fixé.
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 unbound | 184 | 1682 |
| absent svbF7 unbound | 10275 | 120495 |
| in H3K27ac | absent H3K27ac | |
|---|---|---|
| in svbF7 bound | 88 | 280 |
| absent svbF7 bound | 10371 | 109254 |
pvalue_fixe = phyper(88 - 1, 368, 119993 - 368, 10459)
pvalue_nonfixe = phyper(184 - 1, 1866, 132606 - 1866, 10459)
presence = c(88,10371)
absence = c(280,109254)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27ac_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27ac_fixe)
presence = c(184,10275)
absence = c(1682,120495)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27ac_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27ac_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 0.9988463
La pvalue du test de fisher pour les motifs fixé est de 2.205439110^{-18} Celle du test de fisher pour les motifs non fixé est de 0.0021011`
total_svbF7_unbound_H3K27ac = 184 + 1682
total_svbF7_bound_H3K27ac = 88 + 280
percent_svbf7_H3K27ac_unbound = round(100 * 184 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_unbound_without_H3K27ac = round(100 * 1682 / total_svbF7_unbound_H3K27ac, 2 )
percent_svbf7_H3K27ac_bound = round(100 * 88 / total_svbF7_bound_H3K27ac, 2 )
percent_svbf7_bound_without_H3K27ac = round(100 * 280 / total_svbF7_bound_H3K27ac, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K27ac_absent = c(percent_svbf7_bound_without_H3K27ac,percent_svbf7_unbound_without_H3K27ac)
H3K27ac_present = c(percent_svbf7_H3K27ac_bound,percent_svbf7_H3K27ac_unbound)
data_H3K27ac = data.frame(etat_svb,H3K27ac_absent,H3K27ac_present)
datatable(data_H3K27ac,rownames = F,filter = "none",colnames = c("Regions without H3K27ac","Regions with H3K27ac" ))
fig1 = plot_ly(data_H3K27ac, x = ~etat_svb,y = ~H3K27ac_absent, type = "bar",name = "H3K27ac absent")
fig1 = fig1 %>% add_trace(y = ~H3K27ac_present, name = "H3K27ac present")
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb")
fig1
fig1 = plot_ly(data_H3K27ac, x = ~etat_svb,y = ~H3K27ac_absent, type = "bar",name = "H3K27ac absent")
fig1 = fig1 %>% add_trace(y = ~H3K27ac_present, name = "H3K27ac present")
fig1 = fig1 %>% layout(yaxis = list(title = "percent"))
fig1 = fig1 %>% layout(title = "H3K27ac enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig1
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 unbound | 261 | 1605 |
| absent svbF7 unbound | 6345 | 76742 |
| in H3K27me3 | absent H3K27me3 | |
|---|---|---|
| in svbF7 bound | 40 | 328 |
| absent svbF7 bound | 6566 | 72659 |
pvalue_fixe = phyper(40 - 1, 368, 79593 - 368, 6606)
pvalue_nonfixe = phyper(261 - 1, 1866, 84953 - 1866, 6606)
presence = c(40,6566)
absence = c(328,72659)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K27me3_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K27me3_fixe)
presence = c(261,6345)
absence = c(1605,76742)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K27me3_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K27me3_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 0.950963 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 0.0871654 Celle du test de fisher pour les motifs non fixé est de 2.617652810^{-20}`
total_svbF7_unbound_H3K27me3 = 261 + 1605
total_svbF7_bound_H3K27me3 = 40 + 328
percent_svbf7_H3K27me3_unbound = round(100 * 261 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_unbound_without_H3K27me3 = round(100 * 1605 / total_svbF7_unbound_H3K27me3, 2 )
percent_svbf7_H3K27me3_bound = round(100 * 40 / total_svbF7_bound_H3K27me3, 2 )
percent_svbf7_bound_without_H3K27me3 = round(100 * 328 / total_svbF7_bound_H3K27me3, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K27me3_absent = c(percent_svbf7_bound_without_H3K27me3,percent_svbf7_unbound_without_H3K27me3)
H3K27me3_present = c(percent_svbf7_H3K27me3_bound,percent_svbf7_H3K27me3_unbound)
data_H3K27me3 = data.frame(etat_svb,H3K27me3_absent,H3K27me3_present)
datatable(data_H3K27me3,rownames = F,filter = "none",colnames = c("Regions without H3K27me3","Regions with H3K27me3" ))
fig2 = plot_ly(data_H3K27me3, x = ~etat_svb,y = ~H3K27me3_absent, type = "bar",name = "H3K27me3 absent")
fig2 = fig2 %>% add_trace(y = ~H3K27me3_present, name = "H3K27me3 present")
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb")
fig2
fig2 = plot_ly(data_H3K27me3, x = ~etat_svb,y = ~H3K27me3_absent, type = "bar",name = "H3K27me3 absent")
fig2 = fig2 %>% add_trace(y = ~H3K27me3_present, name = "H3K27me3 present")
fig2 = fig2 %>% layout(yaxis = list(title = "percent"))
fig2 = fig2 %>% layout(title = "H3K27me3 enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig2
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 unbound | 263 | 1603 |
| absent svbF7 unbound | 12340 | 118669 |
| in H3K4me1 | absent H3K4me1 | |
|---|---|---|
| in svbF7 bound | 81 | 287 |
| absent svbF7 bound | 12562 | 107325 |
pvalue_fixe = phyper(81 - 1, 368, 120218 - 368, 12606)
pvalue_nonfixe = phyper(263 - 1, 1866, 132875 - 1866, 12603)
presence = c(263,12340)
absence = c(1603,118669)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me1_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me1_fixe)
presence = c(81,12562)
absence = c(287,107325)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me1_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me1_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 1
La pvalue du test de fisher pour les motifs fixé est de 1.235597210^{-10} Celle du test de fisher pour les motifs non fixé est de 1.269695310^{-10}`
total_svbF7_unbound_H3K4me1 = 263 + 1603
total_svbF7_bound_H3K4me1 = 81 + 287
percent_svbf7_H3K4me1_unbound = round(100 * 263 / total_svbF7_unbound_H3K4me1, 2 )
percent_svbf7_unbound_without_H3K4me1 = round(100 * 1603 / total_svbF7_unbound_H3K4me1, 2 )
percent_svbf7_H3K4me1_bound = round(100 * 81 / total_svbF7_bound_H3K4me1, 2 )
percent_svbf7_bound_without_H3K4me1 = round(100 * 287 / total_svbF7_bound_H3K4me1, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K4me1_absent = c(percent_svbf7_bound_without_H3K4me1,percent_svbf7_unbound_without_H3K4me1)
H3K4me1_present = c(percent_svbf7_H3K4me1_bound,percent_svbf7_H3K4me1_unbound)
data_H3K4me1 = data.frame(etat_svb,H3K4me1_absent,H3K4me1_present)
datatable(data_H3K4me1,rownames = F,filter = "none",colnames = c("Regions without H3K4me1","Regions with H3K4me1" ))
fig3 = plot_ly(data_H3K4me1, x = ~etat_svb,y = ~H3K4me1_absent, type = "bar",name = "H3K4me1 absent")
fig3 = fig3 %>% add_trace(y = ~H3K4me1_present, name = "H3K4me1 present")
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb")
fig3
fig3 = plot_ly(data_H3K4me1, x = ~etat_svb,y = ~H3K4me1_absent, type = "bar",name = "H3K4me1 absent")
fig3 = fig3 %>% add_trace(y = ~H3K4me1_present, name = "H3K4me1 present")
fig3 = fig3 %>% layout(yaxis = list(title = "percent"))
fig3 = fig3 %>% layout(title = "H3K4me1 enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig3
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 unbound | 120 | 1746 |
| absent svbF7 unbound | 6646 | 92671 |
| in H3K4me3 | absent H3K4me3 | |
|---|---|---|
| in svbF7 bound | 62 | 306 |
| absent svbF7 bound | 6705 | 86603 |
pvalue_fixe = phyper(62 - 1, 368, 93676 - 368, 6767)
pvalue_nonfixe = phyper(120 - 1, 1866, 101183 - 1866, 6766)
presence = c(120,6646)
absence = c(1746,92671)
svbF7 = c("in svbF7 bound", "absent svbF7 bound")
contingence_H3K4me3_fixe = data.frame(presence,absence, row.names = svbF7)
fisher = fisher.test(contingence_H3K4me3_fixe)
presence = c(120,6646)
absence = c(1746,92671)
svbF7 = c("in svbF7 unbound", "absent svbF7 unbound")
contingence_H3K4me3_nonfixe = data.frame(presence,absence, row.names = svbF7)
fisher_nonfixe = fisher.test(contingence_H3K4me3_nonfixe)
La pvalue du test de hypergéométrique pour les motifs fixé est de 1 Celle du test de hypergéométrique pour les motifs non fixé est de 0.3142804
La pvalue du test de fisher pour les motifs fixé est de 0.7081678 Celle du test de fisher pour les motifs non fixé est de 0.7081678`
total_svbF7_unbound_H3K4me3 = 120 + 1746
total_svbF7_bound_H3K4me3 = 62 + 306
percent_svbf7_H3K4me3_unbound = round(100 * 120 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_unbound_without_H3K4me3 = round(100 * 1746 / total_svbF7_unbound_H3K4me3, 2 )
percent_svbf7_H3K4me3_bound = round(100 * 62 / total_svbF7_bound_H3K4me3, 2 )
percent_svbf7_bound_without_H3K4me3 = round(100 * 306 / total_svbF7_bound_H3K4me3, 2 )
etat_svb = c("svbF7_bound","svb_unbound")
H3K4me3_absent = c(percent_svbf7_bound_without_H3K4me3,percent_svbf7_unbound_without_H3K4me3)
H3K4me3_present = c(percent_svbf7_H3K4me3_bound,percent_svbf7_H3K4me3_unbound)
data_H3K4me3 = data.frame(etat_svb,H3K4me3_absent,H3K4me3_present)
datatable(data_H3K4me3,rownames = F,filter = "none",colnames = c("Regions without H3K4me3","Regions with H3K4me3" ))
fig4 = plot_ly(data_H3K4me3, x = ~etat_svb,y = ~H3K4me3_absent, type = "bar",name = "H3K4me3 absent")
fig4 = fig4 %>% add_trace(y = ~H3K4me1_present, name = "H3K4me3 present")
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb")
fig4
fig4 = plot_ly(data_H3K4me3, x = ~etat_svb,y = ~H3K4me3_absent, type = "bar",name = "H3K4me3 absent")
fig4 = fig4 %>% add_trace(y = ~H3K4me3_present, name = "H3K4me3 present")
fig4 = fig4 %>% layout(yaxis = list(title = "percent"))
fig4 = fig4 %>% layout(title = "H3K4me3 enrichment on svbF7 bound or not by Svb", barmode = "stack")
fig4
rapp_fixe = round((contingence_H3K4me1_fixe[1,1]/total_K4me1_12_16) / (contingence_H3K4me3_fixe[1,1]/total_K4me3_12_16),2)
rapp_nonfixe = round((contingence_H3K4me1_nonfixe[1,1]/total_K4me1_12_16) / (contingence_H3K4me3_nonfixe[1,1]/total_K4me3_12_16),2)
Il y a 1.18 fois de H3K4me1 que de H3K4me3 fixé.
Il y a 0.36 fois de H3K4me1 que de H3K4me3 non fixé.
Lorsque l’on compare les motifs de fixation de Shavenbaby (svbF7 ou ovoQ6) et ses pics de fixation ( embryon, S2 ( sensible ou stringent)) nous observons que 70% à 85% des pics présentent des motifs svbF7 et/ou ovoQ6. Nous observons ensuite que ces motifs présentent des enrichissements en histones différents s’ils sont fixés ou non par Shavenbaby. Dans les cellules S2, les motifs svbF7 fixés par le facteur de transcription présentent un enrichissement en histone H3K27ac, H3K4me1 et H3K4me3. Les motifs fixés présentent un enrichissement en H3K4me1 plus fort qu’en H3K4me3, ce qui laisse à penser que Shavenbaby se fixe sur des régions enhancer préférentiellement. On observe que les motifs svbF7 non fixés en cellules S2 quant à eux présentent un enrichissement moindre en ces marques d’histones voire une absence totale. Ces motifs non fixés présentent un enrichissement en H3K27me3 alors que les motifs fixés n’en présentent pas ou peu. Ces observations sont valables que le motif soit agrandi de 3kb ou 300pb ( taille moyenne des pics). Dans les embryons (8-12h ou 12-16h), les motifs svbF7 fixés par Shavenbaby présentent un enrichissement en H3K4me1 et H3K27ac. Les motifs svbF7 présentent autant d’H3K27me3 ou de H3K4me3 qu’ils soient fixés ou non. En conclusion, les motifs svbF7 fixés présentent un enrichissement en H3K4me1 et H3K27ac qu’on observe en S2 ou en embryon.